Quickly generate a summary table of various alpha level cutoffs.

alphaSummary(object, ...)

# S4 method for DESeqAnalysis
alphaSummary(object, ...)

# S4 method for DESeqDataSet
alphaSummary(
  object,
  alpha = c(0.1, 0.05, 0.01, 0.001, 1e-06),
  contrast = NULL,
  name = NULL
)

Arguments

object

Object.

...

Additional arguments.

alpha

numeric. Multiple alpha cutoffs.

contrast

character. A character vector with exactly 3 elements:

  1. Name of factor in the design formula.

  2. Name of numerator level for the fold change.

  3. Name of denominator level for the fold change.

See DESeq2::results() for details.

name

character(1). Name of the individual effect (coefficient) for building a results table. Use this argument rather than contrast for continuous variables.

Value

integer matrix.

Details

Use either contrast or name to specify the desired contrast.

Note

Updated 2021-03-15.

See also

Author

Michael Steinbaugh, Lorena Patano

Examples

data(deseq) ## DESeqAnalysis ==== alphaSummary(deseq, contrast = c("condition", "B", "A"))
#> condition B A
#> 0.1 0.05 0.01 0.001 1e-06 #> LFC > 0 (up) 48 36 24 15 2 #> LFC < 0 (down) 39 22 14 8 1 #> outliers [1] 0 0 0 0 0 #> low counts [2] 116 116 58 271 0
alphaSummary(deseq, name = "condition_B_vs_A")
#> condition_B_vs_A
#> 0.1 0.05 0.01 0.001 1e-06 #> LFC > 0 (up) 48 36 24 15 2 #> LFC < 0 (down) 39 22 14 8 1 #> outliers [1] 0 0 0 0 0 #> low counts [2] 116 116 58 271 0