test_diffs: test_diffs Statistics function to summarize expression data...

Description Usage Arguments Details Value Author(s) References Examples

Description

generateStats is a summary function used on various expression data, using ratios between selected treatments.

Usage

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test_diffs(cD, groupings= NULL, treatment1=NULL, treatment2=NULL,
mode_mean=TRUE, LOG2=TRUE)

Arguments

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.

Details

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

Value

Returns an invisible list of summary statistics, kruskal test and raw data of a countDat object, using ratios between selected treatments.

Author(s)

AJ Vaestermark, JR Walters.

References

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

Examples

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

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