params: Shared parameter documentation

In steinbaugh/DESeqAnalysis: Acid Genomics DESeq2 Analysis Utilities

Shared parameter documentation

Description

Shared parameter documentation

Arguments

DESeqDataSet	DESeqDataSet or NULL.
DESeqTransform	DESeqTransform.
contrast	character. A character vector with exactly 3 elements: Name of factor in the design formula. Name of numerator level for the fold change. Name of denominator level for the fold change. See DESeq2::results() for details.
contrastSamples	logical(1). Only include the samples used to define the contrast passed to DESeq2::results(). This setting will break for complex DESeq2 contrasts (e.g. interaction effect).
i	character(1) or integer(1). DESeqResults contrast name or position in results slot.
lfcShrink	logical(1) or NULL. Use shrunken log2 fold change (LFC) values. If NULL, inherits value defined in lfcShrink().
limits	list(2). Named list containing "x" and "y" that define the lower and upper limits for each axis. Set automatically by default when left NULL.
name	character(1). Name of the individual effect (coefficient) for building a results table. Use this argument rather than contrast for continuous variables.
results	character(1) or integer(1). Name or position of DESeqResults.

Value

No value.

steinbaugh/DESeqAnalysis documentation built on April 1, 2024, 8:30 a.m.