resultsDEWSeq {DEWSeq} | R Documentation

## extract DEWseq results

### Description

This is a modified version of the `results` function from DESeq2 package.

This function uses chromosomal positions given in the `rowRanges(dds)` to identify overlapping windows in `dds` object. For each window, the number of overlapping windows are counted, and the p-value is adjusted for FWER using bonferroni correction.

For further details, please refer documentation for `results` function in DESeq2 package

### Usage

    resultsDEWSeq(object, contrast, name, listValues = c(1, -1), cooksCutoff,
      test, addMLE = FALSE, tidy = FALSE, parallel = FALSE,
      BPPARAM = bpparam(), minmu = 0.5, start0based = TRUE)

### Arguments

`object` | `DESeqDataSet`, on which the following functions has already been called: `nbinomWaldTest`
`contrast` | `character vector`, `list of 2 character vectors` or `numeric contrast vector` contrast this argument specifies what comparison to extract from the `object` to build a results table, see `results`
`name` | `character`, name the name of the individual effect (coefficient) for building a results table. `name` argument is ignored if `contrast` is specified
`listValues` | `list`, check `results` for details of this parameter
`cooksCutoff` | `numeric`, theshold on Cook's distance
`test` | `character`, this is automatically detected internally if not provided.
`addMLE` | `logical`, if `betaPrior=TRUE` was used
`tidy` | `logical`, whether to output the results table with rownames as a first column 'row'. The table will also be coerced to `data.frame`
`parallel` | `logical`, if FALSE, no parallelization. if TRUE, parallel execution using `BiocParallel`, see next argument `BPPARAM`
`BPPARAM` | `bpparamClass`, an optional parameter object passed internally to `bplapply` when `parallel=TRUE`. If not specified, the parameters last registered with `register` will be used.
`minmu` | `numeric`, lower bound on the estimated count (used when calculating contrasts)
`start0based` | `logical`, TRUE (default) or FALSE. If TRUE, then the start positions in `annotationFile` are considered to be 0-based

### Details

For a detailed description of the column use `mcols(output)$description`

### Value

DESeqResults object

### Examples

    data("slbpDds")
    slbpDds <- estimateSizeFactors(slbpDds)
    slbpDds <- estimateDispersions(slbpDds)
    slbpDds <- nbinomWaldTest(slbpDds)
    slbpWindows <- resultsDEWSeq(slbpDds)

    ## Not run:
    # for a description of the columns in slbpWindows use
    mcols(slbpWindows)$description

    ## End(Not run)

[Package DEWSeq version 1.0.6 Index]