#######################
#' Read in GrandMasterSNPs output
#'
#' @description
#' This reads in single nucleotide polymorphism markers generated
#' by the GrandMasterSNPs Perl program.
#'
#' @param x This is a tab delimited text file from GrandMasterSNPs Perl program
#' @param ... Other arguments passed to the function
#' @keywords read GrandMasterSNPs
#' @return A data frame of GrandMasterSNPs markers
#' @export
#' @examples
#' \dontrun{
#'
#' ##this should be used with the output of the PERL pipeline "GrandMasterSNPs"
#' marker_file <- system.file("extdata/filtered_markers.txt", package = "genotypeR")
#'
#' GrandMasterSNPs_markers <- read_in_Master_SNPs_data(marker_file)
#'}
read_in_Master_SNPs_data <- function(x, ...){
##read in table
out <- read.table(x, stringsAsFactors=FALSE, colClasses=c("character"), sep="\t", ...)
##set column names
colnames(out) <- c("chr", "start", "end", "marker")
##return from function
return(out)
}
#############################################################################################################################
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