Alpha level cutoff summary statistics

Quickly generate a summary table of various alpha level cutoffs.

Usage

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 2023-09-26.

See also

• DESeq2::results().

• DESeq2::resultsNames().

Author

Michael Steinbaugh, Lorena Patano

Examples

data(deseq)

## DESeqAnalysis ====
alphaSummary(deseq, contrast = c("condition", "B", "A"))
#> ℹ condition B A
#>                0.1 0.05 0.01 0.001 1e-06
#> LFC > 0 (up)    39   34   17     3     0
#> LFC < 0 (down)  31   23   13     6     1
#> outliers [1]     0    0    0     0     0
#> low counts [2]  97   49   87     0     0
alphaSummary(deseq, name = "condition_B_vs_A")
#> ℹ condition_B_vs_A
#>                0.1 0.05 0.01 0.001 1e-06
#> LFC > 0 (up)    39   34   17     3     0
#> LFC < 0 (down)  31   23   13     6     1
#> outliers [1]     0    0    0     0     0
#> low counts [2]  97   49   87     0     0