waldUMI4C {UMI4Cats} | R Documentation

## DESeq2 Wald test for differential contacts

### Description

Using a `UMI4C` object, infers the differences between conditions specified in `design` using a Wald Test from `DESeq2` package.

### Usage

    waldUMI4C(
      umi4c,
      query_regions = NULL,
      subset = "sum",
      design = ~condition,
      normalized = TRUE,
      padj_method = "fdr",
      padj_threshold = 0.05
    )

### Arguments

`umi4c` | UMI4C object as generated by `makeUMI4C` or the `UMI4C` constructor.
`query_regions` | `GRanges` object containing the coordinates of the genomic regions you want to use to perform the analysis in specific genomic intervals. Default: NULL.
`subset` | If `query_regions` are provided, how to subset the UMI4C object: "sum" for summing raw UMIs in fragments overlapping `query_regions` (default) or "overlap" for selecting overlapping fragments.
`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, which can be accessed using `resultsUMI4C`.

### Examples

    data("ex_ciita_umi4c")

    umi_dif <- waldUMI4C(ex_ciita_umi4c)

[Package UMI4Cats version 1.2.1 Index]