csaw (version 1.2.1)

SEmethods: Statistical wrappers for SummarizedExperiment objects

Description

Convenience wrappers for statistical routines operating on SummarizedExperiment objects

Usage

normalize(object, ...)
asDGEList(object, ...)

Arguments

object

a SummarizedExperiment object, like that produced by windowCounts

...

other arguments to be passed to the function being wrapped

Value

For normalize, either a numeric matrix or vector is returned; see normalizeCounts.For asDGEList, a DGEList object is returned.

Details

Counts are extracted using the matrix corresponding to the first assay in the SummarizedExperiment object. The total library size is taken from the totals entry in the column data; warnings will be generated if this entry is not present. In the normalize method, the extracted counts and library sizes are supplied to normalizeCounts, along wth arguments in .... Similarly, the asDGEList method wraps the DGEList constructor.

See Also

normalizeCounts, DGEList, windowCounts

Examples

bamFiles <- system.file("exdata", c("rep1.bam", "rep2.bam"), package="csaw")
data <- windowCounts(bamFiles, width=100, filter=1)
normalize(data)
head(normalize(data, type="loess"))

asDGEList(data)
asDGEList(data, norm.factors=c(1.11, 2.23), group=c("a", "b"))