cD.DM: cD.DM Function to convert count dat object to LME4 input.
In avastermark19/doseR_0.99.4: doseR

Description Usage Arguments Details Value Author(s) References Examples

This function generates LME4 input.

1	cD.DM(cD, weightByLL = TRUE)

`cD`	A countDat object containing FPKM values and at least one annotation column.
`weightByLL`	Logical, weigh by log likelihood score.

This function converts count dat object.

Returns LME4 input.

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 = 0.4, hi.bound = 0.5)
dm <- cD.DM(f_hm)