importPairwiseContrasts: Import pairwise contrasts from a file

In acidgenomics/DESeqAnalysis: Acid Genomics DESeq2 Analysis Utilities

Import pairwise contrasts from a file

Description

Import pairwise contrasts from a file

Usage

importPairwiseContrasts(
  file,
  groupCol = "group",
  numeratorCol = "numerator",
  denominatorCol = "denominator",
  namesCol = "description"
)

Arguments

file	character(1). File path.
groupCol	character(1). Group column name in colData() of DESeqDataSet. Corresponds to value in design().
numeratorCol	character(1). Numerator column name in contrasts file.
denominatorCol	character(1). Denominator column name in contrasts file.
namesCol	character(1). Column in contrasts file to used to define the names of the contrast list. Values will be sanitized using snakeCase().

Value

list. Named list of pairwise character vectors containing: "group", "numerator", "denominator".

Note

Updated 2022-05-17.

See Also

DESeq2::results().

Examples

file <- system.file("extdata", "contrasts.csv", package = "DESeqAnalysis")
x <- importPairwiseContrasts(file)
print(x)

acidgenomics/DESeqAnalysis documentation built on June 13, 2025, 10:35 a.m.