validate.plinkfiles <- function(geno.files){
if(!is.data.frame(geno.files) && !is.matrix(geno.files)){
msg <- 'geno.files should be a data frame'
stop(msg)
}
if(is.matrix(geno.files)){
geno.files <- as.data.frame(geno.files)
}
colnames(geno.files) <- convert.header(colnames(geno.files), c('fam', 'bim', 'bed'))
if(!all(c('fam', 'bim', 'bed') %in% colnames(geno.files))){
msg <- 'geno.files should be a data frame with columns \'fam\', \'bim\', \'bed\''
stop(msg)
}
geno.files <- geno.files[, c('fam', 'bim', 'bed')]
fam <- geno.files$fam
cc <- rep('NULL', 6)
cc[1] <- 'character'
for(f in fam){
re <- try(tmp <- load.file(f, header = FALSE, select = cc, nrows = 1e3))
if("try-error" %in% class(re)){
msg <- paste0('Cannot load ', f)
stop(msg)
}
rm(tmp)
gc()
}
bim <- geno.files$bim
cc <- rep('NULL', 6)
cc[2] <- 'character'
for(b in bim){
re <- try(tmp <- load.file(b, header = FALSE, select = cc, nrows = 1e3))
if("try-error" %in% class(re)){
msg <- paste0('Cannot load ', b)
stop(msg)
}
rm(tmp)
gc()
}
geno.files
}
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