rearrangedReadList: Identify rearranged reads - initiallly unmapped reads that...
In cancer-genomics/trellis: Somatic structural variant analysis
rearrangedReadList R Documentation
Identify rearranged reads – initiallly unmapped reads that can be
aligned by blat to span a novel sequence junction.
Description
For unmapped-mapped read pairs where the mapped read is aligned
near a candidate junction, assess whether the unmapped read spans a
novel sequence junctions.
Usage
rearrangedReadList(dirs, rlist, maxgap = 500)
Arguments
dirs
a DataPaths object
rlist
a list of RearrangementList objects
maxgap
a length-one integer vector specifying how much gap
is allowed between a read alignment location and the genomic
intervals for the rearrangement clusters
Value
a list of rearranged reads
cancer-genomics/trellis documentation built on Aug. 20, 2024, 5:48 p.m.
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| rearrangedReadList | R Documentation |
Identify rearranged reads – initiallly unmapped reads that can be aligned by blat to span a novel sequence junction.
Description
For unmapped-mapped read pairs where the mapped read is aligned near a candidate junction, assess whether the unmapped read spans a novel sequence junctions.
Usage
rearrangedReadList(dirs, rlist, maxgap = 500)
Arguments
dirs |
a |
rlist |
a list of |
maxgap |
a length-one integer vector specifying how much gap is allowed between a read alignment location and the genomic intervals for the rearrangement clusters |
Value
a list of rearranged reads
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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