getGenes: List genes involved in present GPS for a specific pathway in...

In sigora: Signature Overrepresentation Analysis

List genes involved in present GPS for a specific pathway in the summary_results

Description

This function lists the genes involved in the present GPS for a pathway of interest, odered by their contribution to the significance of the pathway.

Usage

getGenes(yy, i, idmap = load_data("idmap"))

Arguments

yy	A sigora analysis result object (created by sigora).
i	The rank position of the pathway of interest in summary_results.
idmap	A dataframe for converting between different gene-identifier types (e.g. ENSEMBL, ENTREZ and HGNC-Symbols of genes). Most users do not need to set this argument, as there is a built-in conversion table.

Value

A table (dataframe) with ids of the relevant genes, ranked by their contribution to the statistical significance of the pathway.

See Also

sigora

Examples

data('kegH')
set.seed(seed=12345)
a1 <- genesFromRandomPathways(kegH,3,50)
## originally selected pathways:\cr
a1[["selectedPathways"]]
## what are the genes
a1[["genes"]]
## sigora's results with this input:\cr
sigoraRes <- sigora(GPSrepo = kegH, queryList = a1[["genes"]],level = 2)
## Genes related to the second most significant result:
head(getGenes(sigoraRes,2))

sigora documentation built on March 18, 2022, 8:05 p.m.