cD.DM: cD.DM Function to convert count dat object to LME4 input.

Description Usage Arguments Details Value Author(s) References Examples

Description

This function generates LME4 input.

Usage

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cD.DM(cD, weightByLL = TRUE)

Arguments

cD

A countDat object containing FPKM values and at least one annotation column.

weightByLL

Logical, weigh by log likelihood score.

Details

This function converts count dat object.

Value

Returns LME4 input.

Author(s)

AJ Vaestermark, JR Walters.

References

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

Examples

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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)

avastermark19/doseR_0.99.4 documentation built on May 6, 2019, 12:08 p.m.