hbTests-methods {GGtools} | R Documentation |
haplotype-block based tests for structured expression variation
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
.)
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))]]