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Base mean threshold

Source: R/AllGenerics.R, R/degPerContrast-methods.R
degPerContrast.Rd

Base mean threshold

Usage

degPerContrast(object, ...)

# S4 method for DESeqAnalysis
degPerContrast(
  object,
  i = NULL,
  direction = c("both", "up", "down"),
  return = c("matrix", "list")
)

Arguments

object

Object.

i

character, numeric, or NULL. Names or range of results. If set NULL, include all results.

direction

character(1). Include "both", "up", or "down" directions.

return

character(1). Return type. Uses match.arg() internally and defaults to the first argument in the character vector.

...

Additional arguments.

Value

  • matrix: Matrix containing numbers of DEGs per contrast. Intended primarily for use with plotDegStackedBar().

  • list: Named vector containing the DEG identifiers. Intended primarily for use with plotDegUpset().

Note

Updated 2022-05-18.

Examples

data(deseq)

## DESeqAnalysis ====
degPerContrast(deseq)
#>      condition_B_vs_A treatment_D_vs_C
#> down               13                0
#> up                 17                0