Description Usage Arguments Details Value Author(s) References Examples
This function is an LME4 wrapper for dosage analysis.
1 |
dm |
The dm data. Generally a reformatted countDat object from cD.DM. |
model |
The model. Expressed using standard LME4 syntax, see vignette. |
... |
passthrough arguments. |
This function is an lme4 wrapper.
Returns LME4 output.
AJ Vaestermark, JR Walters.
The "doseR" package, 2018 (in press).
1 2 3 4 5 6 7 8 9 10 11 12 13 | 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)
glSeq(dm, "-1 + replicate")
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