Nothing
#############################################################################################################################
#' Make reference/alternate allele table from make_marker_names output
#'
#' @description
#' \code{Ref_Alt_Table} makes the ref/alt table used
#' in for proper genotype coding and
#' QA/QC \code{initialize_genotypeR_data}.
#'
#' @param markers_in_study make_marker_names output
#' @keywords make_marker_names
#' @return A data frame of Ref/Alt genotypes
#' @export
#' @examples
#'
#' data(markers)
#' markers_in_study <- make_marker_names(markers)
#' genotype_table <- Ref_Alt_Table(markers_in_study = markers_in_study)
#'
Ref_Alt_Table <- function(markers_in_study){
##look for ATCG at the [Ref/Alt] in the marker from GrandMasterSNPs.pl
SNP_list <- regmatches(markers_in_study$marker, gregexpr("[A|T|C|G]\\/[A|T|C|G]", markers_in_study$marker))
##split up into Ref and Alt
SNP_df <- data.frame(do.call(rbind, strsplit(do.call(rbind, SNP_list), split="/")), stringsAsFactors=FALSE)
colnames(SNP_df) <- c("Ref", "Alt")
##make Alt_Ref geno
SNP_df$Alt_Ref <- paste(SNP_df$Alt, SNP_df$Ref, sep="")
##make Ref_Alt geno
SNP_df$Ref_Alt <- paste(SNP_df$Ref, SNP_df$Alt, sep="")
##add marker names
SNP_df$marker_names <- markers_in_study$marker_names
####################################################################
sort_SNPs <- function(SNP_df){
genotype_table <- SNP_df
##sort
genotype_table$sort_position <- as.numeric(do.call(rbind, strsplit(genotype_table$marker_names, "_(?=[0-9])", perl=TRUE))[,2])
genotype_table$sort_chr <- do.call(rbind, strsplit(genotype_table$marker_names, "_(?=[0-9])", perl=TRUE))[,1]
sorted_df <- genotype_table[order(genotype_table$sort_chr, genotype_table$sort_position),]
out_sorted_df <- sorted_df[,colnames(SNP_df)]
return(out_sorted_df)
}
sorted_SNP_df <- sort_SNPs(SNP_df=SNP_df)
####################################################################
return(sorted_SNP_df)
}
#############################################################################################################################
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.