calc_hyper: Perform hypergeometric test

Description Usage Arguments Value Examples

View source: R/calc_hyper.R

Description

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

Usage

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calc_hyper(df, listDf, intersectDf, 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

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## Not run: 
# an example


## End(Not run)

frhl/genoppi-v4 documentation built on May 5, 2020, 7:16 a.m.