plotMA.CD: plotMA.CD Function to make MA plot.

In avastermark19/doseR_0.99.4: doseR

Description

This function generates MA plot.

Usage

plotMA.CD(cD, samplesA, samplesB, scale = NULL,
xlab = "A", ylab = "M", ...)

Arguments

cD	A countDat object.
samplesA	Either a character vector, identifying sample set A by either replicate name or sample name, or a numerical vector giving the columns of data in the 'countDat' object that forms sample set A.
samplesB	Either a character vector, identifying sample set B by either replicate name or sample name, or a numerical vector giving the columns of data in the 'countDat' object that forms sample set B.
scale	If given, defines the scale on which the log-ratios will be plotted.
xlab	Label for the X-axis. Defaults to "A".
ylab	Label for the Y-axis. Defaults to "M".
...	Any other parameters to be passed to the plot function.

Details

This function makes MA plot from count dat object.

Value

Returns MA plot.

Author(s)

AJ Vaestermark, JR Walters.

References

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

Examples

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)
plotMA.CD(hm, samplesA = 'Male', samplesB = 'Female')

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