testLocality: Test local upregulation

Description Usage Arguments Value Examples

View source: R/analyze.R

Description

Tests for local upregulation locally in certain directions

Usage

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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

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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)

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

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