Nothing
#' @title mhc_check
#' @description this function only contains the alleles list, read by netMHCpan,
#' the list was retrieved by reading the file exported from netMHCpan, using the
#' following command line "netMHCpan -listMHC"
#' @param netmhcpan_alleles the netmhcpan alleles to be used for the netmhcpan call.
#' @details a custom error is printed in case the allele is not written correctly
#' @return
#' \itemize{
#' \item returns a custom error message if MHC/HLA allele(s) are not
#' written correctly
#' \item returns nothing if there are no issues. If HLA alleles are not
#' written correctly}
#' @examples
#' if (interactive()) {
#' mhc_check("HLA-A02:01")
#' mhc_check("HLA-A0201")
#' }
#' @rdname mhc_check
#' @export
mhc_check<- function(netmhcpan_alleles){
#retrieve netMHCpan list of alleles
netmhcpan_listofalleles<- netmhcpan_list_alleles$V1
#re-format the input alleles
if (length(grep("\\*", netmhcpan_alleles))==0){
}else{
netmhcpan_alleles<- gsub("\\*", "", netmhcpan_alleles)
}
#check if alleles are in netmhcpan list of alleles
x <- sapply(strsplit(netmhcpan_alleles,split=","), function(y) {
ifelse(y %in% netmhcpan_listofalleles, TRUE, FALSE)})
if (all(x)) {
#nothing returned if all good.
}else{
stop(" Please check the input alleles:", netmhcpan_alleles[x==FALSE])
}
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.