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]