het_haplo: Haplotype heterozygosity rate

In genostats/gaston.pop: Gaston package extension for genetic population applications

Description

Global and by SNP Fst computation for given populations

Usage

 het.haplo(x, map=c('B36','B37'), block=0.5, minl=1, maxl=+Inf, thread=1)

Arguments

x	A bed.matrix
map	Recombinaison map. Must be B36, B37 or a data.frame contains 'chr', 'base', 'rate.cM.Mb' and 'cM' variables". If B36, we use recombinaison map from Hapmap contained in genmapB36. If B37, we use recombinaison map from 1000 Genomes contained in genmapB37.
block	Maximum recombinaison value in cM/Mb to define haplotype blocks
minl	Minimum length of haplotype block
maxl	Maximum length of haplotype block
thread	Number of used thread

Details

Haplotype frequencies are estimated using EM algorithm available in haplo.stats package.

Value

A List of 22 elements, one by autosomal chromosoms. Each element is a list of two with: - a vector with heterozygotie rate by considered haplotype blocks. - a list which gives for each haplotype blocks ids of considered SNP.

Author(s)

Claire Dandine-Roulland

Examples

# load chr2 data set (~10k SNPs in low LD)
x <- set.stats(read.bed.matrix( system.file("extdata", "chr2.bed", package="gaston") ))

# Compute Fst
het <- het.haplo(x, map='B37', block=0.5, minl=1, maxl=+Inf, thread=1)
str(het)

genostats/gaston.pop documentation built on Jan. 17, 2022, 10:58 a.m.