sigora (version 3.0.5)

genesFromRandomPathways: 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(seed = 1234, GPSrepo, np, ng)

Arguments

seed

A random seed.

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

# NOT RUN {
## select 50 genes from 3 human KEGG pathways
a1<-genesFromRandomPathways(seed=12345,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
# }