runXtail: xtail analysis wrapper for 'SummarizedExperiment' objects

In xryanglab/xtail: Genome-wide assessment of differential translations with ribosome profiling data

xtail analysis wrapper for SummarizedExperiment objects

Description

The xtail function can be used directly with SummarizedExperiment objects. The mrna and rpf data must be stored as two separate assays.

Usage

runXtail(x, mrna_assay, rpf_assay, ...)

## S4 method for signature 'SummarizedExperiment'
runXtail(x, mrna_assay, rpf_assay, ...)

addXtail(x, ...)

## S4 method for signature 'SummarizedExperiment'
addXtail(x, ...)

Arguments

x	a RpfSummarizedExperiment object
mrna_assay	a scalar character. The name of the assay containing the mRNA data.
rpf_assay	a scalar character. The name of the assay containing the rpf data.
...	For runXtail: additional parameters passed on to xtail. For addXtail: additional parameters passed on to runXtail and xtail.

Details

See xtail for more details on the analysis function.

Value

A xtail object for runXtail or an object of class(x).

Examples

data(xtaildata)
test.mrna <- xtaildata$mrna[1:100,]
test.rpf <- xtaildata$rpf[1:100,]
condition <- c("control","control","treat","treat")

se <- SummarizedExperiment(assays = list(mrna = test.mrna, rpf = test.rpf),
                           colData = DataFrame(condition = condition))
xtail <- runXtail(se, "mrna", "rpf", condition = colData(se)$condition,
                  bins = 1000, threads = 2)
xtail

se <- addXtail(se, "mrna", "rpf", condition = colData(se)$condition,
               bins = 1000, threads = 2)
rowData(se)

xryanglab/xtail documentation built on April 13, 2022, 2:34 p.m.