Combine GRanges coverage replicates
combineGRcoverage( gr, covNames = NULL, covName = NULL, strands = NULL, scaleFactors = 1, verbose = FALSE, ... )
gr | GRanges object containing coverage data in columns containing NumericList class data. |
---|---|
covNames | character vector of |
covName | character vector with length equal to
|
strands | character vector, or NULL, indicating the strand
for which the coverage data was obtained. When |
scaleFactors | numeric vector length equal to |
verbose | logical indicating whether to print verbose output. |
... | additional arguments are ignored. |
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
.
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.
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()