hbTests-methods {GGtools}R Documentation

haplotype-block based tests for structured expression variation

Description

haplotype-block based tests for structured expression variation

Methods

fmla = "genesym", sms = "smlSet", cnum = "chrnum", rsid = "numeric", rad = "numeric"
expression data for gene identified by genesym is extracted from sms, and genotype data within rad base pairs of rsid are obtained and processed by mapLD to define haplotype blocks and the SNP tagging these blocks. Score tests are then computed for the association of expression of the gene identified by genesym with haplotype copy number (additive model by default, but options captured by ... are passed to haplo.score.)

Examples

library(GGtools)
data(hmceuB36.2021)
hmFou = hmceuB36.2021[, hmceuB36.2021$isFounder==TRUE]
hh = hbTests(genesym("CPNE1"), hmFou, chrnum(20), 33600000, 2e4 )
hh
pvals(hh)
plot(locs(hh), -log10(pvals(hh)))
hscores(hh)[[which.min(pvals(hh))]]

[Package GGtools version 3.2.0 Index]