compareZscores: Compare the Z scores of individual GO terms between two input...

In sam-bassett/CompGO: An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation

Description

Accepts two fnAnot charts as args, does z score and p value calculations on them and returns a data.frame with important data. A flag, geneInfo, is provided in case the user wants to get information about the intersection and union of genes corresponding to the individual GO terms. Importantly, this function does some implicit thresholding: only terms with a minimum of 'cutoff' genes are compared, and any term present in one list but not the other is discarded.

Usage

compareZscores(setA, setB, geneInfo = FALSE, cutoff = 10)

Arguments

setA	FunctionalAnnotationChart to compare
setB	FunctionalAnnotationChart to compare
geneInfo	Whether to add gene intersection and union info to the data.frame
cutoff	The minimum number of genes to threshold terms by

Value

A data.frame with columns: Term, Zscore.A, Zscore.B, ComparedZ, Pvalue (optionally geneUnion, geneIntersect as well, which are comma-separated strings).

Examples

data(funChart1)
data(funChart2)
cz = compareZscores(funChart1, funChart2)
str(cz)
cz = compareZscores(funChart1, funChart2, geneInfo = TRUE)
str(cz)

sam-bassett/CompGO documentation built on May 29, 2019, 1:01 p.m.