resultsDEWSeq: extract DEWseq results

In EMBL-Hentze-group/DEWSeq: Differential Expressed Windows Based on Negative Binomial Distribution

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)

EMBL-Hentze-group/DEWSeq documentation built on Oct. 17, 2023, 10:41 p.m.