R/convert.snp.ped.R

In GenABEL: genome-wide SNP association analysis

"convert.snp.ped" <- 
		function(pedfile,mapfile,outfile,format="premakeped",traits=1,
				strand="u",bcast=10000000,wslash=FALSE,mapHasHeaderLine=TRUE) 
{
	
	alcodes <- alleleID.codes()
	
	poss <- c("u","+","-","file")
	intstrand <- which(poss == strand)-1
	if (length(intstrand)!=1) {cat("strand argument must be one of",poss,"\n");stop();}
	
# strand == 0 -> unknown ('u')
# strand == 1 -> plus ('+')
# strand == 2 -> minus ('-')
# extendedmap -> five columns (chr,name,pos,strand,coding) expected in map-file
# passed through intstrand <- 3 !
	
	posf <- c("premakeped","mach")
	intfmt <- which(posf == format)-1
	if (length(intfmt)!=1) {cat("format argument must be one of",posf,"\n");stop();}
	
# intfmt = 0 -> premakeped, merlin
# else -> mach
	
	if (wslash) {
		.C("convert_snp_merlin_wslash",as.character(pedfile),as.character(mapfile),
				as.character(outfile),as.integer(intstrand),as.integer(bcast),
				as.character(alcodes),as.integer(length(alcodes)),as.integer(intfmt),
				as.integer(traits),as.integer(mapHasHeaderLine),
				PACKAGE="GenABEL")
	} else {
		.C("convert_snp_merlin",as.character(pedfile),as.character(mapfile),
				as.character(outfile),as.integer(intstrand),as.integer(bcast),
				as.character(alcodes),as.integer(length(alcodes)),as.integer(intfmt),
				as.integer(traits),as.integer(mapHasHeaderLine),
				PACKAGE="GenABEL")
	}
	return(invisible(0))
}