hapmap.read.haplotypes: Read hapmap haplotypes.

In gtx: Genetics ToolboX

Description

Reads HapMap haplotypes and legend and stores in format expected by functions in gtx package.

Usage

hapmap.read.haplotypes(chr, path, sample = "CEU", release = 22)

Arguments

chr	chromosome to read
path	path to local mirror of ftp://ftp.ncbi.nlm.nih.gov/hapmap
sample	a HapMap sample, e.g. CEU or YRI
release	a HapMap release version, currently must be 21 or 22

Details

You need a local mirror of HapMap data. To build this use e.g. a shell command
rsync ftp://ftp.ncbi.nlm.nih.gov/hapmap ~
then use an argument path="~/hapmap" for this function call.

Technically the local mirror only needs the contents of
ftp://ftp.ncbi.nlm.nih.gov/hapmap/phasing/2006-07_phaseII/phased/
and
ftp://ftp.ncbi.nlm.nih.gov/hapmap/phasing/2007-08_rel22/phased/

Other gtx functions expect to be passed a list with 22 elements; one for each chromosome. See the examples.

Author(s)

Toby Johnson [e-mail]

Examples

## Not run: 
## chromosomes 1-22
hapmap <- lapply(1:22, hapmap.read.haplotypes, path = "~/hapmap")

## selected chromosomes only
hapmap <- lapply(1:22, function() return(NULL))
for (chr in c(1, 11, 17)) {
  hapmap[[chr]] <- hapmap.read.haplotypes(chr, path = "~/hapmap")
}

## End(Not run)

gtx documentation built on May 2, 2019, 5:08 a.m.