getLibsizes-methods: getLibsizes method for count Dat class, derived from...
In avastermark19/doseR_0.99.4: doseR

Description Usage Arguments Value Examples

getLibsizes method for count Dat class, derived from getLibsizes1 method (countData class).

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getLibsizes2(cD, subset = NULL,
estimationType = c("quantile", "total",
"edgeR"),quantile = 0.75, ...)

`cD`	A count Dat object.
`subset`	Value
`estimationType`	e.g. quantile, total, edgeR.
`quantile`	A quantile, expressed as e.g. 0.75.
`...`	Passthrough arguments.

Libsize value

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,replicates=reps,
seglens=hm.tr,annotation=annotxn)
libsizes(hm) <- getLibsizes2(hm, estimationType = "total")
getLibsizes2(hm)