degComps {DEGreport}R Documentation

Automatize the use of results() for multiple comparisons

Description

This function will extract the output of DESeq2::results() and DESeq2::lfcShrink() for multiple comparison using:

Usage

degComps(dds, combs = NULL, contrast = NULL, alpha = 0.05,
  skip = FALSE, type = "normal", pairs = FALSE)

Arguments

dds

DESeq2::DESeqDataSet obcject.

combs

Optional vector indicating the coefficients or columns fom colData(dds) to create group comparisons.

contrast

Optional vector to specify contrast. See DESeq2::results().

alpha

Numeric value used in independent filtering in DESeq2::results().

skip

Boolean to indicate whether skip shrinkage. For instance when it comes from LRT method.

type

Type of shrinkage estimator. See DESeq2::results().

pairs

Boolean to indicate whether create all comparisons or only use the coefficient already created from DESeq2::resultsNames().

Details

Value

DEGSet with unSrunken and Srunken results.

Author(s)

Lorena Pantano

Examples

library(DESeq2)
dds <- makeExampleDESeqDataSet(betaSD=1)
colData(dds)[["treatment"]] <- sample(colData(dds)[["condition"]], 12)
  design(dds) <-  ~ condition + treatment
dds <- DESeq(dds)
res <- degComps(dds, combs = c("condition", 2),
              contrast = list("treatment_B_vs_A", c("condition", "A", "B")))

[Package DEGreport version 1.18.1 Index]