plink <- function(...) {
values <- c(...)
args <- names(values)
plink <- plink_version()
program_on_path("plink")
if(is.null(args)) args <- ""
commands <- ifelse(args == "", values, paste(args, values))
commands <- paste(commands, collapse = " ")
system(paste(plink, commands))
}
plink_version <- function(){
plink_v <- gsub(".*v(\\S..).*", "\\1", system('plink --version', T))
if (plink_v >= 1.9) {
plink_v <- "plink"
} else {
plink_v <- "plink --noweb"
}
return(plink_v)
}
read.bim <- function(bim_file, header = F, col.names = c("CHR","SNP","GD","POS","A1", "A2"), colClasses = c("integer", "character", "numeric", "integer", rep("character", 2)), ...) {
data.table::fread(bim_file, header = F, col.names = col.names, colClasses = colClasses, ...)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.