degResults {DEGreport} | R Documentation

## Complete report from DESeq2 analysis

### Description

Complete report from DESeq2 analysis

### Usage

    degResults(
      res = NULL,
      dds,
      rlogMat = NULL,
      name,
      org = NULL,
      FDR = 0.05,
      do_go = FALSE,
      FC = 0.1,
      group = "condition",
      xs = "time",
      path_results = ".",
      contrast = NULL
    )

### Arguments

`res` | output from `DESeq2::results()` function.
`dds` | `DESeq2::DESeqDataSet()` object.
`rlogMat` | matrix from `DESeq2::rlog()` function.
`name` | string to identify results
`org` | an organism annotation object, like org.Mm.eg.db. NULL if you want to skip this step.
`FDR` | int cutoff for false discovery rate.
`do_go` | boolean if GO enrichment is done.
`FC` | int cutoff for log2 fold change.
`group` | string column name in colData(dds) that separates samples in meaninful groups.
`xs` | string column name in colData(dss) that will be used as X axes in plots (i.e time)
`path_results` | character path where files are stored. NULL if you don't want to save any file.
`contrast` | list with character vector indicating the fold change values from different comparisons to add to the output table.

### Value

ggplot2 object

### Examples

    data(humanGender)
    library(DESeq2)
    idx <- c(1:10, 75:85)
    dse <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:1000, idx],
      colData(humanGender)[idx,], design=~group)
    dse <- DESeq(dse)
    res <- degResults(dds = dse, name = "test", org = NULL,
      do_go = FALSE, group = "group", xs = "group", path_results = NULL)

[Package DEGreport version 1.28.0 Index]