| 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)