testLocality: Test local upregulation

In saeyslab/triwise: Gene expression changes in three biological conditions

Description

Tests for local upregulation locally in certain directions

Usage

testLocality(Goi, Gdiffexp, angles, deltangle = pi/24,
  bandwidth = pi/3)

Arguments

Goi	Gene set for which to test enrichment
Gdiffexp	Differentially expressed genes
angles	Numeric vector with angles of all genes or a dataframe as returned by 'transformBarycentric'
deltangle	Stepsize of angles
bandwidth	Bandwidth of angles

Value

Corrected p-values for enrichment around every angle

Examples

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)

Goi = 1:50
qvals = testLocality(Goi, Gdiffexp=(1:1000)[barycoords$r > 1], barycoords)
plot(attr(qvals, "anglesoi"), qvals)

saeyslab/triwise documentation built on May 29, 2019, 12:56 p.m.