testUnidirectionality: Test gene sets for unidirectional enrichment

Description Usage Arguments Value Examples

View source: R/analyze.R

Description

Test gene sets for unidirectional enrichment

Usage

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testUnidirectionality(barycoords, gsets, Gdiffexp = NULL,
  statistic = "diffexp", bm = NULL, minknown = 5, mindiffexp = 0,
  maxknown = 1500, mc.cores = getOption("mc.cores", default = 1), ...)

Arguments

barycoords

Dataframe containing for every gene its barycentric coordinates, as returned by transformBarycentric

gsets

List of character vectors, each containing a set of genes (gene identifiers)

Gdiffexp

Differentially expressed genes

statistic

A string denoting the measure used for the strength of upregulation of a particular gene.

  • diffexp: Whether a gene is differentially expressed (1 versus 0)

  • rank: The rank of the maximal log fold-change

  • r: The maximal log fold-change

  • z: Custom using the z-column within barycoords

  • angle: Uses a rayleigh z-test ignoring non-differentially expressed genes within the gene set

bm

Previously calculated background model using the generateBackgroundModel

minknown

Minimal number of genes within a gene set for it to be considered for enrichment

mindiffexp

Minimal number of genes differentially expressed within a gene set for it to be considered for enrichment

maxknown

Maximal number of genes within a gene set for it to be considered for enrichment

mc.cores

Number of processor cores to use. Due to limitations of the parallel package, this does not work on Windows

...

Parameters for generateBackgroundModel

Value

Dataframe containing for every gene set which passed the filtering:

Examples

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Eoi = matrix(rnorm(1000*3, sd=0.5), 1000, 3, dimnames=list(1:1000, c(1,2,3)))
Eoi[1:100,1] = Eoi[1:100,1] + 4 # the first 100 genes are more upregulated in the first condition
barycoords = transformBarycentric(Eoi)

gsets = list(a=1:50, b=80:150, c=200:500)
testUnidirectionality(barycoords, gsets, Gdiffexp=(1:1000)[barycoords$r > 1])

Zouter/triwise documentation built on June 3, 2017, 10:50 a.m.