R: Print Summary Statistics of Alpha Level Cutoffs

degSummary {DEGreport}

R Documentation

Print Summary Statistics of Alpha Level Cutoffs

Description

Print Summary Statistics of Alpha Level Cutoffs

Usage

degSummary(
  object,
  alpha = c(0.1, 0.05, 0.01),
  contrast = NULL,
  caption = "",
  kable = FALSE
)

Arguments

`object`	Can be DEGSet or DESeqDataSet or DESeqResults.
`alpha`	Numeric vector of desired alpha cutoffs.
`contrast`	Character vector to use with `results()` function.
`caption`	Character vector to add as caption to the table.
`kable`	Whether return a `knitr::kable()` output. Default is data.frame.

Value

data.frame or knitr::kable().

Author(s)

Lorena Pantano

References

original idea of multiple alpha values and code syntax from Michael Steinbaugh.

Examples

library(DESeq2)
data(humanGender)
idx <- c(1:5, 75:80)
counts <- assays(humanGender)[[1]]
dse <- DESeqDataSetFromMatrix(counts[1:1000, idx],
                              colData(humanGender)[idx,],
                              design = ~group)
dse <- DESeq(dse)
res1 <- results(dse)
res2 <- degComps(dse, contrast = c("group_Male_vs_Female"))
degSummary(dse, contrast = "group_Male_vs_Female")
degSummary(res1)
degSummary(res1, kable = TRUE)
degSummary(res2[[1]])

[Package DEGreport version 1.23.3 Index]