snpm2phase {GGtools}R Documentation

convert information in a snp.matrix to PHASE input format; invokePhase can run a suitably installed version of PHASE

Description

convert information in a snp.matrix to PHASE input format; invokePhase can run a suitably installed version of PHASE

Usage

snpm2phase(snpm, cnum, outfilename)
parsePh.out(fn)
personalHap(x)

Arguments

snpm snp.matrix instance
cnum chromosome number as chrnum instance
outfilename character name of file to write
fn character name of PHASE .out file to read
x output of parsePh.out

Details

follows phase 2.1 documentation for input format

a phaseInput container class can store relevant metadata

Value

writes to a file and gives a message

Author(s)

Vince Carey <stvjc@channing.harvard.edu>

Examples

data(smtest)
tt = tempfile()
pin = snpm2phase(smtest, chrnum(20), tt)

class(pin)
getClass("phaseInput")
pin
readLines(tt)
unlink(tt)
pp = parsePh.out(system.file("phaseOut/cpne1_20k.out", package="GGtools"))
pp[[1]][1:3]
personalHap(pp)

[Package GGtools version 3.2.0 Index]