addSingleGeneSets: Adds a collection of single-gene psuedo-sets.

In franapoli/gep2pep: Creation and Analysis of Pathway Expression Profiles (PEPs)

Description

This function can be used to add single-gene (as opposed to pathway) -based collections. Sets including a single gene don't need to go through normal Kolmogorov-Smirnov statistic computation and are treated differently for performance.

Usage

addSingleGeneSets(rp, genes, organism = "Homo Sapiens")

Arguments

rp	A repository created by createRepository.
genes	a character vector containing the gene names. For each og them a single-gene GeneSet will be created.
organism	Character vector used to annotate the created sets. "Homo Sapiens" by default.

Details

Enrichment Scores and p-values for sets including a single gene are computed with dedicated (fast) routines. Although a statistic based on a single gene is not efficient per se, it is useful to have data in the same format as pathway-based profiles. buildPEPs internally calls single gene dedicated routines whenever a gene set collection is tagged (see repo function tag) with "SGE" ("Single Gene Expression"), which is done automatically by addSingleGeneSets. In that case, the min_size parameter is ignored.

Value

Nothing, used for side effects.

See Also

buildPEPs

Examples

db <- loadSamplePWS()
repo_path <- file.path(tempdir(), "gep2pepTemp")

rp <- createRepository(repo_path, db)

## The following will create PEPs in 2 separate files
geps <- loadSampleGEP()
addSingleGeneSets(rp, rownames(geps))

unlink(repo_path, TRUE)

franapoli/gep2pep documentation built on May 30, 2019, 4:34 p.m.