loadESmatrix: Loads the matrix of Enrichment Scores for a collection

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

Description

Loads the matrix of Enrichment Scores for a collection

Usage

loadESmatrix(rp, collection)

Arguments

rp	A repository created by createRepository.
collection	One of the names returned by getCollections.

Value

The matrix of Enrichment Scores (ES) of the Kolmogorov-Smirnov statistic for the pathway collection, if previously computed with buildPEPs. The entry i,j reports the ES for the pathway i, conditionj. If buildPEPs was not run, throws an error.

Examples

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

rp <- createRepository(repo_path, db)
geps <- loadSampleGEP()
buildPEPs(rp, geps)

loadESmatrix(rp, "c3_TFT")[1:5,1:2]

unlink(repo_path, TRUE)

gep2pep documentation built on Nov. 8, 2020, 5:59 p.m.