contrastSamples: Samples corresponding to a differential expression contrast

Description Usage Arguments Details Value Note Examples

Description

Samples corresponding to a differential expression contrast

Usage

1
2
3
4
contrastSamples(object, ...)

## S4 method for signature 'DESeqAnalysis'
contrastSamples(object, i, ...)

Arguments

object

Object.

i

Indices specifying elements to extract or replace. Indices are numeric or character vectors, empty (missing), or NULL.

For more information:

help(topic = "Extract", package = "base")
...

Additional arguments.

Details

Match the samples in a DESeqDataSet used to define contrast in a corresponding DESeqResults object. Note that this only works for simple (e.g. pairwise) contrasts and will intentionally error for more complex comparisons.

Value

character. Sample identifiers.

Note

Updated 2020-08-04.

EXPERIMENTAL. This approach will error intentionally for DESeqResults objects generated with complex contrasts (e.g. interaction effect or LRT). It may be removed in a future release if this approach is too error-prone.

Examples

1
2
3
4
data(deseq)

## DESeqAnalysis ====
contrastSamples(deseq, i = 1L)

steinbaugh/DESeqAnalysis documentation built on Sept. 25, 2020, 5:21 a.m.