combineGRcoverage: Combine GRanges coverage replicates

In jmw86069/splicejam: Analysis and Visualization of Gene Splice Variants and Transcriptome Data

Combine GRanges coverage replicates

Description

Combine GRanges coverage replicates

Usage

combineGRcoverage(
  gr,
  covNames = NULL,
  covName = NULL,
  strands = NULL,
  scaleFactors = 1,
  verbose = FALSE,
  ...
)

Arguments

gr	GRanges object containing coverage data in columns containing NumericList class data.
covNames	character vector of colnames(GenomicRanges::values(gr)) representing columns in gr that contain coverage data in NumericList format, for example data prepared with getGRcoverageFromBw().
covName	character vector with length equal to length(covNames) representing the sample_id for each covNames entry.
strands	character vector, or NULL, indicating the strand for which the coverage data was obtained. When NULL the strand is inferred by the presence of any negative values.
scaleFactors	numeric vector length equal to length(covNames) or expanded to that length. Values are multiplied by each coverage data result, intended to apply a normalization to each coverage value. A -1 value can also be used to flip the score of negative strand data, in the event the source coverage data is scored only using positive values.
verbose	logical indicating whether to print verbose output.
...	additional arguments are ignored.

Details

This function takes a GRanges object as output from getGRcoverageFromBw() and combines the coverages into one coverage per strand for each covName (equivalent to sample_id). Each coverage value is multiplied by its scaleFactors value, then the sum is returned for each strand, for each covName (sample_id).

The strand is inferred by the presence of negative values, where any negative value indicates the column is negative strand.

Value

GRanges object whose colnames contain the covName (sample_id) for each observed strand, with coverage combined taking the sum of individual coverages after multiplying each by scaleFactors.

See Also

Other jam GRanges functions: addGRLgaps(), addGRgaps(), annotateGRLfromGRL(), annotateGRfromGR(), assignGRLexonNames(), closestExonToJunctions(), exoncov2polygon(), findOverlapsGRL(), flattenExonsBy(), getFirstStrandedFromGRL(), getGRLgaps(), getGRcoverageFromBw(), getGRgaps(), grl2df(), jam_isDisjoint(), make_ref2compressed(), sortGRL(), spliceGR2junctionDF(), stackJunctions()

Other jam RNA-seq functions: assignGRLexonNames(), closestExonToJunctions(), defineDetectedTx(), detectedTxInfo(), exoncov2polygon(), flattenExonsBy(), getGRcoverageFromBw(), groups2contrasts(), internal_junc_score(), makeTx2geneFromGtf(), make_ref2compressed(), prepareSashimi(), runDiffSplice(), sortSamples(), spliceGR2junctionDF()

jmw86069/splicejam documentation built on Nov. 4, 2024, 10:53 a.m.