genesFromRandomPathways: Function to randomly select genes associated with randomly...

In sigora: Signature Overrepresentation Analysis

Function to randomly select genes associated with randomly pathways.

Description

This function first randomly selects a number (np) of pathways, then randomly selects a number (ng) of genes that are associated with at least one of the selected pathways. The function can be used to compare Sigora's performance to traditional overrepresentation tests.

Usage

genesFromRandomPathways(GPSrepo, np, ng)

Arguments

GPSrepo	A signature repository (created by ..) or one of the precompiled options.
np	How many pathways to select.
ng	Number of genes to be selected.

Value

selectedPathways	A vector containing the "np" originally selected pathways.
genes	A vector containing the "ng" selected genes from selectedPathways.

References

Foroushani AB, Brinkman FS and Lynn DJ (2013).“Pathway-GPS and SIGORA: identifying relevant pathways based on the over-representation of their gene-pair signatures.”PeerJ, 1

See Also

sigora-package

Examples

data('kegH')
## select 50 genes from 3 human KEGG pathways
seed=1234
set.seed(seed)
a1 <- genesFromRandomPathways(kegH,3,50)
## originally selected pathways:
a1[["selectedPathways"]]
## what are the genes
a1[["genes"]]
## sigora's results
sigoraRes <- sigora(GPSrepo =kegH, queryList = a1[["genes"]],
        level = 4)
## compare to traditional methods results:
oraRes <- ora(a1[["genes"]],kegH)
dim(oraRes)
oraRes

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