loadESmatrix: Loads the matrix of Enrichment Scores for a collection

Description Usage Arguments Value Examples

View source: R/gep2pep.R

Description

Loads the matrix of Enrichment Scores for a collection

Usage

1
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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
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.