#' A function to subset the data
#'
#' This function will subset the data by RNAseq counts.
#'
#' @param data data.frame.
#' @param feature character string indicating the column that has the feature (gene)
#' @param genotype character string indicating the column that has the genotype identifier
#' @param mean_threshold minimum mean count across samples for a feature to be included
#' @param count_threshold minimum count in any sample for a feature to be included
#'
#' @export
#' @return The subsetted data frame
#' @author Jarad Niemi
#'
trim = function(data, feature="feature", genotype="genotype", mean_threshold=1, count_threshold=0) {
if (!require(plyr)) {
warning("Please install the plyr library.\nNo trimming performed.")
return(data)
}
ddply(data, feature, function(x) {
if (any(x$count < count_threshold)) return(NULL)
if (mean(x$count) < mean_threshold ) return(NULL)
return(x)
})
}
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