enrichment_in_abundance

Enrichment in abundance calculates enrichment in pathways by the difference in abundance of the pathway members.

Usage

enrichment_in_abundance(
  geneset,
  eset,
  assay_name,
  mapping_column = NULL,
  abundance_column = NULL,
  fdr = 0,
  matchset = NULL,
  sample_comparison = NULL,
  min_p_threshold = NULL,
  sample_n = NULL,
  silence_try_errors = TRUE
)

Arguments

geneset

Gene set to calculate enrichment

eset

Molecular abundance data in `SummarizedExperiment` format

assay_name

Name of assay to compare

mapping_column

Column to use to map identifiers

abundance_column

Columns to use to quantify abundance

fdr

number of times to sample for FDR value

matchset

Name of a set to use for enrichment

sample_comparison

list of samples to use as comparison. if missing background (eset) is used

min_p_threshold

Only include p-values lower than this

sample_n

size of sample to use

silence_try_errors

set to true to silence try errors

Value

data frame of enrichment result