dafs: dafs
In avastermark19/doseR_0.99.4: doseR

Description Usage Arguments Details Value Author(s) References Examples

This function filters the expression using DAFS (see ref). This is a core function invoked by the DAFS wrapper.

1	dafs(VEC1, PLOT)

`VEC1`	Vector 1, not intended for user interaction.
`PLOT`	Boolean, toggles plotting.

This function filters the expression, using Data Adaptive Flag method.

Returns vx[which.min(vv)] to wrapper function.

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)