snpm2phase {GGtools} | R Documentation |
convert information in a snp.matrix to PHASE input format; invokePhase can run a suitably installed version of PHASE
snpm2phase(snpm, cnum, outfilename) parsePh.out(fn) personalHap(x)
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 |
follows phase 2.1 documentation for input format
a phaseInput container class can store relevant metadata
writes to a file and gives a message
Vince Carey <stvjc@channing.harvard.edu>
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)