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 1.4.4
Index]