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 1.30.3 Index]