degComps {DEGreport} | R Documentation

## Automatize the use of `results()` for multiple comparisons

### Description

This function will extract the output of `DESeq2::results()` and `DESeq2::lfcShrink()` for multiple comparison using:

### Usage

    degComps(
      dds,
      combs = NULL,
      contrast = NULL,
      alpha = 0.05,
      skip = FALSE,
      type = "normal",
      pairs = FALSE,
      fdr = "default"
    )

### Arguments

`dds` | DESeq2::DESeqDataSet obcject.
`combs` | Optional vector indicating the coefficients or columns fom `colData(dds)` to create group comparisons.
`contrast` | Optional vector to specify contrast. See `DESeq2::results()`.
`alpha` | Numeric value used in independent filtering in `DESeq2::results()`.
`skip` | Boolean to indicate whether skip shrinkage. For instance when it comes from LRT method.
`type` | Type of shrinkage estimator. See `DESeq2::lfcShrink()`.
`pairs` | Boolean to indicate whether create all comparisons or only use the coefficient already created from `DESeq2::resultsNames()`.
`fdr` | type of fdr correction. `default` is FDR value, `lfdr-stat` is for local FDR using the statistics of the test, `lfdr-pvalue` is for local FDR using the p-value of the test. fdrtools needs to be installed and loaded by the user

### Details

- coefficients

- contrast

- Multiple columns in `colData` that match coefficients

- Multiple columns in `colData` to create all possible contrasts

### Value

DEGSet with unSrunken and Srunken results.

### Author(s)

Lorena Pantano

### Examples

    library(DESeq2)
    dds <- makeExampleDESeqDataSet(betaSD=1)
    colData(dds)[["treatment"]] <- sample(colData(dds)[["condition"]], 12)
      design(dds) <-  ~ condition + treatment
    dds <- DESeq(dds)
    res <- degComps(dds, combs = c("condition", 2),
                    contrast = list("treatment_B_vs_A", c("condition", "A", "B")))
    # library(fdrtools)
    #res <- degComps(dds,contrast = list("treatment_B_vs_A"),
    #                fdr="lfdr-stat")

[Package DEGreport version 1.28.0 Index]