calc_hyper: Perform hypergeometric test

In lagelab/Genoppi: genoppi

Perform hypergeometric test

Description

Use one-tailed hypergeometric test to calculate overlap enrichment between proteomic data and other datasets (e.g. InWeb, gene lists, etc.)

Usage

calc_hyper(df, listDf, intersectDf = data.frame(intersectN = T), bait = NULL)

Arguments

df	data.frame containing proteomic data, with gene and significant columns
listDf	data.frame containing data to overlap, with listName, gene and significant columns
intersectDf	data.frame contaning listName and intersectN columns intersectN = vector of boolean variables indicating if total population should be intersect of the two datasets
bait	name of bait protein

Value

list of data.frame and list. Data.frame contains list_name, successInSample_count (x), sample_count (n), notSample_count (N-n), success_count (k), population_count (N), pvalue. List of lists (for each listName) contains genes names corresponding to each group (successInSample_genes, sample_genes, notSample_genes, success_genes, population_genes).

Examples

## Not run: 
data("example_data")
inwebDf <- get_inweb_list('BCL2')
inwebDf$listName <- 'list1'
intersectDf <- data.frame(listName='list1', intersectN = T)
calc_hyper(example_data, inwebDf, intersectDf, 'BCL2')

## End(Not run)

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