generateStats: generateStats Statistics function to summarize expression...
In avastermark19/doseR_0.99.4: doseR

Description Usage Arguments Details Value Author(s) References Examples

generateStats is a summary function used on various expression data.

1	generateStats(cD, groupings= NULL, mode_mean=TRUE, LOG2=TRUE)

`cD`	A countDat object.
`groupings`	A grouping (annotation column), e.g. groupings="something".
`mode_mean`	Boolean, Calculate RowMeans or RowMedians.
`LOG2`	Boolean, Calculate LOG2.

This function completes summary statistics of the expression of the supplied countDat object.

Returns an invisible list of summary statistics, kruskal test and raw data of a countDat object.

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)
generateStats(hm, groupings='Chromosome')