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Import pairwise contrasts from a file

Source: R/importPairwiseContrasts.R
importPairwiseContrasts.Rd

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)
#> → Importing /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/Rtmp084QYu/temp_libpath90db7851a19c/DESeqAnalysis/extdata/contrasts.csv using base::`read.table()`.
print(x)
#> $dox_induction_control
#>       group   numerator denominator 
#>     "group"         "B"         "A" 
#> 
#> $effect_of_wt_protein_induction_vs_ev_line
#>       group   numerator denominator 
#>     "group"         "C"         "B" 
#>