dafsFilter: dafsFilter Function to filter expression data within a cD...
In avastermark19/doseR_0.99.4: doseR

Description Usage Arguments Details Value Author(s) References Examples

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.

1	dafsFilter(cD, PLOT=TRUE)

`cD`	A countDat object.
`PLOT`	Boolean, toggles plotting.

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).

Returns an invisible, filtered countDat object.

AJ Vaestermark, JR Walters.

BMC Bioinformatics, 2014, 15:92

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)