Description Usage Arguments Details Value Author(s) References Examples
This function generates MA plot.
1 2 |
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. |
This function makes MA plot from count dat object.
Returns MA plot.
AJ Vaestermark, JR Walters.
The "doseR" package, 2018 (in press).
1 2 3 4 5 6 7 8 9 10 11 | 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')
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.