R/dafsFilter.R

In avastermark19/doseR_0.99.4: doseR

#' @title dafsFilter Function to filter expression data within a cD object.
#' @description This function filters the expression of the supplied
#' countDat object, by invoking the dafsFilter (dafs) function. dafsFilter is a
#' filtering function used to remove rows (genes) of various expression data.
#' @usage dafsFilter(cD, PLOT=TRUE)
#' @param cD A countDat object.
#' @param PLOT Boolean, toggles plotting.
#' @details This function filters the expression of the supplied cD object
#' using a Data Adaptive Flag filter. The internal function uses a vector
#' to store Kolmogorov Smirnov distance statistics, loops through cuts of
#' the data to determine targeted K-S statistic, selects data greater than
#' a quantile and runs Mclust on that data to determine theoretical
#' distribution. The wrapper uses simpleFilter to determine first left-most
#' local minima (using the Earth library).
#' @return Returns an invisible, filtered countDat object.

#' @examples
#' library(mclust)
#' library(edgeR)
#' data(hmel.data.doser)
#' reps <- c("Male", "Male", "Male", "Female", "Female", "Female")
#' annotxn <- data.frame("Chromosome" = factor(hmel.dat$chromosome,
#' levels = 1:21))
#' hm.tr<-hmel.dat$trxLength
#' hm<-new("countDat",data=hmel.dat$readcounts,seglens=hm.tr,
#' annotation=annotxn)
#' replicates(hm) <- reps
#' libsizes(hm) <- getLibsizes2(hm, estimationType = "total")
#' rpkm(hm) <- make_RPKM(hm)
#' f_hm <- dafsFilter(hm)

#' @author AJ Vaestermark, JR Walters.
#' @references BMC Bioinformatics, 2014, 15:92

dafsFilter <- function(cD, PLOT=TRUE) {

VEC1 <- rowMeans(cD@RPKM)

cutoff <- dafs (VEC1, PLOT)

invisible(   simpleFilter(cD, mean_cutoff=2^cutoff, counts=FALSE    )    )

}