lapply_calc_hyper: lapply calc_hyper to multiple datasets

In lagelab/Genoppi: genoppi

lapply calc_hyper to multiple datasets

Description

calculate hypergeometric enrichment of genes in tissue and subsequent adjusting for multiple testing.

Usage

lapply_calc_hyper(
  data,
  reference,
  col.by = "tissue",
  bait = NULL,
  p.adj.method = "fdr",
  intersectN = T,
  verbose = F
)

Arguments

data	proteomic data with gene and significant columns.
reference	table with col.by, gene, significant in columns.
col.by	string. What column contains the group?
bait	bait. String. Passed to ?calc_hyper.
p.adj.method	Default is fdr. See p.adjust.methods in ?stats::p.adjust.
intersectN	Boolean indicating if the total population should be the intersect of the two datasets, when calculating hypergeometric overlap.
verbose	print out progress

Examples

## Not run: 
# check for enrichment in GTEx
data(gtex_table)
data(example_data)
data = example_data %>% calc_mod_ttest %>% id_significant_proteins()
gtex_enrichment = lapply_calc_hyper(data, gtex_table)
gtex_enrichment

## End(Not run)

lagelab/Genoppi documentation built on Oct. 13, 2022, 2:36 p.m.