plotRatioBoxes: plotRatioBoxes Function to boxplot density of ratios between...
In avastermark19/doseR_0.99.4: doseR

Description Usage Arguments Details Value Author(s) References Examples

This function plots the expression of the supplied countDat object, representing ratios between a pair of selected treatments as a boxplot for each group in the selected annotation column.

1 2	plotRatioBoxes(cD, groupings= NULL, treatment1=NULL, treatment2=NULL, mode_mean=TRUE, LOG2=TRUE, ...)

`cD`	A countDat object.
`groupings`	A grouping (annotation column), e.g. groupings="something".
`treatment1`	Symbol, treatment 1.
`treatment2`	Symbol, treatment 2.
`mode_mean`	Boolean, Calculate RowMeans or RowMedians.
`LOG2`	Boolean, Calculate LOG2.
`...`	Passthrough arguments to boxplot (additional arguments affecting the summary produced).

This function boxplots expression of the supplied countDat object using ratios of treatment1/treatment2.

Returns an invisible data frame containing the values.

AJ Vaestermark, JR Walters.

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

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)
plotRatioBoxes(hm, groupings='Chromosome', treatment1 = 'Male',
treatment2 = 'Female')