nbinomWaldTestUMI4C {UMI4Cats} | R Documentation

## Differential UMI4C contacts using DESeq2 Wald Test

### Description

Takes the smooth monotone fit count values and infers the differential UMI4C contacts using DESeq2 Wald Test from `DESeq2` package.

### Usage

    nbinomWaldTestUMI4C(dds, query_regions = NULL)

### Arguments

`dds` | DDS object as generated by `smoothMonotoneUMI4C` with the smooth monotone fit counts
`query_regions` | `GRanges` object or `data.frame` containing the coordinates of the genomic regions you want to use to perform the analysis in specific genomic intervals. Default: NULL.

### Details

This function back-transform fitted values to the scale of raw counts and scale them across the samples to obtain normalized factors using `normalizationFactors` from `DESeq2` package. To detect differences between conditions, the DESeq2

### Value

DDS object with the DESeq2 Wald Test results, with results columns accessible with the `results` function.

[Package UMI4Cats version 1.2.1 Index]