pctOverlap: calculate percent overlap between two GRanges objects
In alyssafrazee/ballgown-release: Flexible, isoform-level differential expression analysis
Description
Usage
Arguments
Details
Value
Author(s)
Examples
Description
calculate percent overlap between two GRanges objects
Usage
1
pctOverlap(tx1, tx2)
Arguments
tx1
GRanges object
tx2
GRanges object
Details
In the ballgown context, tx1 and tx2 are two
transcripts, each represented by GRanges objects whose ranges represent the
exons comprising the transcripts. The percent overlap is the number of
nucleotides falling within both transcripts divided by the number of
nucleotides falling within either transcript. Useful as a measure of
transcript closeness (as it is essentially Jaccard distance).
Value
percent overlap between tx1 and tx2, as defined by the
ratio of the intersection of tx1 and tx2 to the union of
tx1 and tx2.
Author(s)
Alyssa Frazee
Examples
1
2
3
4
data(bg)
gtfPath = system.file('extdata', 'annot.gtf.gz', package='ballgown')
annot_grl = gffReadGR(gtfPath, splitByTranscript=TRUE)
pctOverlap(structure(bg)$trans[[2]], annot_grl[[369]]) #79.9%
alyssafrazee/ballgown-release documentation built on May 12, 2019, 1:40 a.m.
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Description Usage Arguments Details Value Author(s) Examples
Description
calculate percent overlap between two GRanges objects
Usage
1 | pctOverlap(tx1, tx2)
|
Arguments
tx1 |
GRanges object |
tx2 |
GRanges object |
Details
In the ballgown context, tx1 and tx2 are two
transcripts, each represented by GRanges objects whose ranges represent the
exons comprising the transcripts. The percent overlap is the number of
nucleotides falling within both transcripts divided by the number of
nucleotides falling within either transcript. Useful as a measure of
transcript closeness (as it is essentially Jaccard distance).
Value
percent overlap between tx1 and tx2, as defined by the
ratio of the intersection of tx1 and tx2 to the union of
tx1 and tx2.
Author(s)
Alyssa Frazee
Examples
1 2 3 4 | data(bg)
gtfPath = system.file('extdata', 'annot.gtf.gz', package='ballgown')
annot_grl = gffReadGR(gtfPath, splitByTranscript=TRUE)
pctOverlap(structure(bg)$trans[[2]], annot_grl[[369]]) #79.9%
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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