quantFilter: quantFilter Function to filter expression data of a countDat...
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; quantFilter is a filtering function used to remove rows (genes) of various expression data.

1 2	quantFilter (cD, lo.bound=.25, hi.bound=.75, MEDIAN = FALSE, na.rm = TRUE)

`cD`	A countDat object.
`lo.bound`	The lower cutoff, expressed as a percentage.
`hi.bound`	The upper cutoff, expressed as a percentage.
`MEDIAN`	Boolean, Calculate RowMeans or RowMedians.
`na.rm`	Boolean, NA removal.

This function filters the expression of the supplied countDat object, based on a selected percentage cutoff.

Returns a filtered countDat object.

AJ Vaestermark, JR Walters.

The "doseR" package, 2018 (in press).

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 <- quantFilter(hm, lo.bound=0.5)