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Calculate functional or pathway enrichment

enrich_ora.Rd

enrich_ora() calculates over-representation statistics (ORA) using an interest list of genes from differential expression results in spammR and gene sets (either the ones provided in spammR or user supplied) This function uses results from calc_spatial_diff_ex. Interest list of genes for ORA is obtained from spatialDiffEx results based on the criteria specified in this function.It is a wrapper for the leapR package which is required For ORA using an external or already defined interest list of genes and gene sets, use leapR functions directly

Usage

enrich_ora(
  spe,
  geneset,
  feature_column,
  pval_type_forThresh = "adjusted_pval",
  pval_thresh = 0.05,
  logFC_lowerThresh = NA,
  logFC_upperThresh = NA,
  geneset_name = "msigdb",
  sortResultsBy,
  comparison_name = ""
)

Arguments

spe

SpatialExperiment object containing spatial omics data and spatial diffex results

geneset

in GMT format

feature_column

Column of rowData that maps to gene set

pval_type_forThresh

Choose from "adjusted_pval" or "pval". Type of p-value that should be used for filtering statistically significant results. Default is adjusted p-value for multiple hypotheses correction.

pval_thresh

value to use for filtering based on pval_type_forThreshold. Default is 0.05. Values less than pval_thresh will be kept.

logFC_lowerThresh

Lower threshold for log Fold Change, to be used for filtering spatialDiffEx results. Default is NA

logFC_upperThresh

Upper threshold for log Fold Change, to be used for filtering spatialDiffEx results. Default is NA

geneset_name

Name of geneset provided

sortResultsBy

For sorting ORA results, choose from the following column names: "BH_pvalue" (default)

comparison_name

Example: "RSPv_vs_others" Text to indicate in results data frame, which spatial groups were compared for the interest list of genes

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)
pooledPanc <- dplyr::bind_cols(smallPancData)
panc.spe <- convert_to_spe(pooledPanc, pancMeta, protMeta, 
feature_meta_colname = "pancProts")
#> Spatial object created without spatial coordinate 
#>          column names provided. Distance based analysis will not be enabled.
#> Note: Only mapping metadata for 2986 features out of 3000 data points
diffex.spe <- calc_spatial_diff_ex(panc.spe, category_col = "IsletOrNot")
#> Warning: Partial NA coefficients for 2 probe(s)
#> We found 0 features with a logFC greater than 1 and 
#>                  an ajusted p-value less than 0.05
library(leapR)
data("krbpaths")
ora.res <- enrich_ora(diffex.spe, geneset = krbpaths, 
         geneset_name = "krbpaths", feature_column = "PrimaryGeneName")