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

Description Usage Arguments Value See Also Examples

View source: R/getGenes.R

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

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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

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a1<-genesFromRandomPathways(seed=12345,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:
getGenes(sigoraRes,2)

sigora documentation built on Aug. 24, 2019, 1:04 a.m.