deseq2UMI4C {UMI4Cats} | R Documentation

## DDS object to UMI4Cats object.

### Description

Transforms an DDS object to a UMI4C object after applying `nbinomWaldTestUMI4C`.

### Usage

    deseq2UMI4C(
      umi4c,
      dds,
      design = ~condition,
      normalized = TRUE,
      padj_method = "fdr",
      padj_threshold = 0.05
    )

### Arguments

`umi4c` | UMI4C object as generated by `makeUMI4C` or the `UMI4C` constructor.
`dds` | DDS object as generated by `nbinomWaldTestUMI4C` with the DESeq2 Wald Test results
`design` | A `formula` or `matrix`. The formula expresses how the counts for each fragment end depend on the variables in `colData`. See `DESeqDataSet`.
`normalized` | Logical indicating if the function should return normalized or raw UMI counts. Default: TRUE.
`padj_method` | The method to use for adjusting p-values, see `p.adjust`. Default: fdr.
`padj_threshold` | Numeric indicating the adjusted p-value threshold to use to define significant differential contacts. Default: 0.05.

### Value

UMI4C object with the DESeq2 Wald Test results.

[Package UMI4Cats version 1.0.1 Index]