Nothing
write.plink <- function(gp,wdir=getwd(),prefix=paste(substitute(gp)),ld.threshold=0,type=c("data.frame","matrix"),ld.window=99999){
# information from arguments
geno <- gp$geno
n <- nrow(geno)
M <- ncol(geno)
# recode genotypic data
geno[geno==0] <- "BB" ##? or "AA"
geno[geno==2] <- "AA"
geno[geno==1] <- "AB"
# prepare .ped file
# family ID, individual ID, paternal ID, maternal ID, sex, phenotype, genotypedata
# we omit cols 3-6
if(is.null(family)){
warning("missing family information in gpData$covar")
gp$covar$family <- 1
}
family <- gp$covar$family[gp$covar$genotyped] # only for individuals with genotypes
id <- gp$covar$id[gp$covar$genotyped] # only for individuals with genotypes
# combine in one file
ped <- data.frame(family,id,geno)
# prepare .map file
# Chromosome ID, SNP ID, genetic distance, bp pos
chr <- gp$map$chr
if (length(chr)!=M) stop("PLINK does not allow different number of markers in 'map' and 'geno'")
snpID <- rownames(gp$map)
gPos <- bpPos <- gp$map$pos
#else gPos <- rep(0,M)
#if(gp$info$map.unit=="bp") bpPos <- gp$map$pos
#else bpPos <- rep(0,M)
# combine in one file
map <- data.frame(chr,snpID,gPos,bpPos)
# write data for PLINK
write.table(ped,file=file.path(wdir,paste(prefix,".ped",sep="")),quote=FALSE,col.names=FALSE,row.names=FALSE)
write.table(map,file=file.path(wdir,paste(prefix,".map",sep="")),quote=FALSE,col.names=FALSE,row.names=FALSE)
# write PLINK script (sink does not work for Linux)
#zz <- file(file.path(wdir,paste(prefix,"plinkScript.txt",sep="")), open="wt")
#sink(zz)
#cat("--ped ",prefix,".ped \n",sep="",append=TRUE)
#cat("--map ",prefix,".map \n",sep="",append=TRUE)
#cat("--compound-genotypes \n")
#cat("--out ",prefix,"\n")
#cat("--no-parents \n")
#cat("--no-sex \n")
#cat("--no-pheno \n")
#cat("--allow-no-sex \n")
#if(type=="matrix") cat("--matrix \n")
#else {
# cat("--ld-window 99999\n")
# cat("--ld-window-r2 ",ld.threshold)
#}
#cat("--r2 \n")
#sink()
#unlink(file.path(wdir,paste(prefix,"plinkScript.txt",sep="")))
cat("--ped ",prefix,".ped \n","--map ",prefix,".map \n","--compound-genotypes \n","--out ",prefix,"\n","--no-parents \n","--no-sex \n","--no-pheno \n","--allow-no-sex \n",ifelse(type=="matrix","--matrix \n",paste("--ld-window ",nrow(map),"\n","--ld-window-kb ",ld.window,"\n","--ld-window-r2 ",ld.threshold,"\n",sep="")),"--r2 \n",sep="",file=file.path(wdir,paste(prefix,"plinkScript.txt",sep="")))
}
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