Skip to contents

Calculate functional or pathway enrichment from a gradient

enrich_gradient.Rd

enrich_gradient() calculates over-representation statistics (ORA) using a ranking of genes from distance_based_analysis() For ORA using an external or already defined interest list of genes and gene sets, use leapR functions directly

Usage

enrich_gradient(spe, assay_name, geneset, feature_column, ranking_column)

Arguments

spe

SpatialExperiment object containing spatial omics data and spatial diffex results

assay_name

name of assay

geneset

in GMT format

feature_column

Column of rowData that maps to gene set

ranking_column

Column of rowData that maps to ranks

Value

A dataframe containing results from over-representation analysis of members of gene sets in the interest list of genes based on filtering criteria above.

Examples

data(smallPancData)
data(pancMeta)
data(protMeta)
img0.spe <- convert_to_spe(smallPancData$Image_0,
  pancMeta,
  protMeta,
  feature_meta_colname = "pancProts",
  image_files = system.file("extdata", "Image_0.png", package = "spammR"),
  image_sample_ids = "Image0",
  spatial_coords_colnames = c("x_pixels", "y_pixels"),
  sample_id = "Image0",
  image_ids = "Image0"
)
#> Note: Only mapping metadata for 2986 features out of 3000 data points
img0.spe <- distance_based_analysis(img0.spe,
  "proteomics",
  sampleCategoryCol = "IsletOrNot",
  sampleCategoryValue = "Islet"
)
library(leapR)
data("krbpaths")
rank.res <- enrich_gradient(img0.spe,
  geneset = krbpaths,
  feature_column = "PrimaryGeneName",
  ranking_column = "IsletDistancespearmanCor"
)
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
head(rank.res)
#>                                                                ingroup_n
#> REACTOME_CHOLESTEROL_BIOSYNTHESIS                                     11
#> REACTOME_STEROID_METABOLISM                                           18
#> BIOCARTA_ACTINY_PATHWAY                                               12
#> BIOCARTA_SALMONELLA_PATHWAY                                           10
#> REACTOME_ACTIVATION_OF_THE_AP1_FAMILY_OF_TRANSCRIPTION_FACTORS         6
#> REACTOME_FORMATION_OF_PLATELET_PLUG                                   79
#>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            ingroupnames
#> REACTOME_CHOLESTEROL_BIOSYNTHESIS                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 TM7SF2, FDFT1, LSS, MVD, HSD17B7, MVK, LBR, EBP, PMVK, NSDHL, CYP51A1
#> REACTOME_STEROID_METABOLISM                                                                                                                                                                                                                                                                                                                                                                                                                                    SLC27A2, ABCC3, CYP7B1, TM7SF2, ALB, SCP2, FDFT1, LSS, FABP6, HSD17B4, MVD, HSD17B7, MVK, LBR, EBP, PMVK, NSDHL, CYP51A1
#> BIOCARTA_ACTINY_PATHWAY                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  WASL, PIR, PSMA7, ARPC1B, ARPC2, ARPC3, ARPC5, NCK1, ARPC4, ACTR3, ACTR2, RAC1
#> BIOCARTA_SALMONELLA_PATHWAY                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         WASL, ARPC1B, ARPC2, ARPC3, ARPC5, ARPC4, CDC42, ACTR3, ACTR2, RAC1
#> REACTOME_ACTIVATION_OF_THE_AP1_FAMILY_OF_TRANSCRIPTION_FACTORS                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  JUN, MAPK3, MAPK1, MAPK8, MAPK9, MAPK14
#> REACTOME_FORMATION_OF_PLATELET_PLUG                            STXBP3, LEFTY2, PDPK1, ACTN4, CALU, GNG7, WDR1, SOD1, F13A1, SERPINA1, A2M, TIMP1, COL1A1, APOA1, FGA, FGB, FGG, FN1, ALB, TF, ALDOA, VWF, GNAI2, APP, SERPING1, ITGB1, FYN, PSAP, PFN1, LYN, THBS1, COL1A2, GNAI3, CD63, CALM1, CLU, HSPA5, ACTN1, SRC, LAMP2, PECAM1, CD36, PRKCA, ITGA2, PTPN1, VCL, FLNA, CD9, CFL1, DGKA, PIK3R1, GNA11, FCER1G, AKT1, AKT2, ACTN2, CSK, SYK, CRK, GNAQ, VAV2, GNG2, RAP1B, GNB1, GNB2, PPIA, GRB2, GNAI1, GNG5, TUBA4A, CAP1, GNA12, PTK2, STX4, DGKZ, GNA13, ITPR2, ITPR1, MAPK14
#>                                                                ingroup_mean
#> REACTOME_CHOLESTEROL_BIOSYNTHESIS                                 0.4810512
#> REACTOME_STEROID_METABOLISM                                       0.3811838
#> BIOCARTA_ACTINY_PATHWAY                                          -0.3818871
#> BIOCARTA_SALMONELLA_PATHWAY                                      -0.4278824
#> REACTOME_ACTIVATION_OF_THE_AP1_FAMILY_OF_TRANSCRIPTION_FACTORS   -0.4207286
#> REACTOME_FORMATION_OF_PLATELET_PLUG                               0.1837898
#>                                                                outgroup_n
#> REACTOME_CHOLESTEROL_BIOSYNTHESIS                                    2982
#> REACTOME_STEROID_METABOLISM                                          2982
#> BIOCARTA_ACTINY_PATHWAY                                              2982
#> BIOCARTA_SALMONELLA_PATHWAY                                          2982
#> REACTOME_ACTIVATION_OF_THE_AP1_FAMILY_OF_TRANSCRIPTION_FACTORS       2982
#> REACTOME_FORMATION_OF_PLATELET_PLUG                                  2982
#>                                                                outgroup_mean
#> REACTOME_CHOLESTEROL_BIOSYNTHESIS                                 0.03500242
#> REACTOME_STEROID_METABOLISM                                       0.03500242
#> BIOCARTA_ACTINY_PATHWAY                                           0.03500242
#> BIOCARTA_SALMONELLA_PATHWAY                                       0.03500242
#> REACTOME_ACTIVATION_OF_THE_AP1_FAMILY_OF_TRANSCRIPTION_FACTORS    0.03500242
#> REACTOME_FORMATION_OF_PLATELET_PLUG                               0.03500242
#>                                                                    zscore
#> REACTOME_CHOLESTEROL_BIOSYNTHESIS                               1.1516930
#> REACTOME_STEROID_METABOLISM                                     0.8634470
#> BIOCARTA_ACTINY_PATHWAY                                        -0.9864392
#> BIOCARTA_SALMONELLA_PATHWAY                                    -1.0279462
#> REACTOME_ACTIVATION_OF_THE_AP1_FAMILY_OF_TRANSCRIPTION_FACTORS -3.0356160
#> REACTOME_FORMATION_OF_PLATELET_PLUG                             0.3493178
#>                                                                 oddsratio
#> REACTOME_CHOLESTEROL_BIOSYNTHESIS                               0.5946843
#> REACTOME_STEROID_METABOLISM                                     0.4592357
#> BIOCARTA_ACTINY_PATHWAY                                        -0.5164099
#> BIOCARTA_SALMONELLA_PATHWAY                                    -0.5584059
#> REACTOME_ACTIVATION_OF_THE_AP1_FAMILY_OF_TRANSCRIPTION_FACTORS -0.6135856
#> REACTOME_FORMATION_OF_PLATELET_PLUG                             0.1933453
#>                                                                     pvalue
#> REACTOME_CHOLESTEROL_BIOSYNTHESIS                              0.002992787
#> REACTOME_STEROID_METABOLISM                                    0.004281058
#> BIOCARTA_ACTINY_PATHWAY                                        0.004512856
#> BIOCARTA_SALMONELLA_PATHWAY                                    0.005475967
#> REACTOME_ACTIVATION_OF_THE_AP1_FAMILY_OF_TRANSCRIPTION_FACTORS 0.007849053
#> REACTOME_FORMATION_OF_PLATELET_PLUG                            0.008232740
#>                                                                BH_pvalue
#> REACTOME_CHOLESTEROL_BIOSYNTHESIS                              0.8515129
#> REACTOME_STEROID_METABOLISM                                    0.8515129
#> BIOCARTA_ACTINY_PATHWAY                                        0.8515129
#> BIOCARTA_SALMONELLA_PATHWAY                                    0.8515129
#> REACTOME_ACTIVATION_OF_THE_AP1_FAMILY_OF_TRANSCRIPTION_FACTORS 0.8534607
#> REACTOME_FORMATION_OF_PLATELET_PLUG                            0.8534607
#>                                                                SignedBH_pvalue
#> REACTOME_CHOLESTEROL_BIOSYNTHESIS                                    0.8515129
#> REACTOME_STEROID_METABOLISM                                          0.8515129
#> BIOCARTA_ACTINY_PATHWAY                                             -0.8515129
#> BIOCARTA_SALMONELLA_PATHWAY                                         -0.8515129
#> REACTOME_ACTIVATION_OF_THE_AP1_FAMILY_OF_TRANSCRIPTION_FACTORS      -0.8534607
#> REACTOME_FORMATION_OF_PLATELET_PLUG                                  0.8534607
#>                                                                background_n
#> REACTOME_CHOLESTEROL_BIOSYNTHESIS                                        NA
#> REACTOME_STEROID_METABOLISM                                              NA
#> BIOCARTA_ACTINY_PATHWAY                                                  NA
#> BIOCARTA_SALMONELLA_PATHWAY                                              NA
#> REACTOME_ACTIVATION_OF_THE_AP1_FAMILY_OF_TRANSCRIPTION_FACTORS           NA
#> REACTOME_FORMATION_OF_PLATELET_PLUG                                      NA
#>                                                                background_mean
#> REACTOME_CHOLESTEROL_BIOSYNTHESIS                                           NA
#> REACTOME_STEROID_METABOLISM                                                 NA
#> BIOCARTA_ACTINY_PATHWAY                                                     NA
#> BIOCARTA_SALMONELLA_PATHWAY                                                 NA
#> REACTOME_ACTIVATION_OF_THE_AP1_FAMILY_OF_TRANSCRIPTION_FACTORS              NA
#> REACTOME_FORMATION_OF_PLATELET_PLUG                                         NA