get_improper_readpairs: Extract all improperly paired reads from an object with...
In cancer-genomics/trellis: Somatic structural variant analysis
View source: R/alignment-utils.R
get_improper_readpairs R Documentation
Extract all improperly paired reads from an object with queryRanges defined
Description
This function is a wrapper for readGAlignments followed by
makeGAlignmentPairs2. Only read pairs in which both the first read
and the last read in a pair overlap with the queryRanges are
returned. Note, a given read pair need not overlap the same
queryRange. To allow fuzzy matching of alignments to the
queryRanges, the queryRanges are expanded by 2kb in each direction.
Usage
get_improper_readpairs(object, bam.file)
Arguments
object
An object for which queryRanges method is defined
bam.file
The complete file path to a bam file.
cancer-genomics/trellis documentation built on Aug. 20, 2024, 5:48 p.m.
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View source: R/alignment-utils.R
| get_improper_readpairs | R Documentation |
Extract all improperly paired reads from an object with queryRanges defined
Description
This function is a wrapper for readGAlignments followed by makeGAlignmentPairs2. Only read pairs in which both the first read and the last read in a pair overlap with the queryRanges are returned. Note, a given read pair need not overlap the same queryRange. To allow fuzzy matching of alignments to the queryRanges, the queryRanges are expanded by 2kb in each direction.
Usage
get_improper_readpairs(object, bam.file)
Arguments
object |
An object for which |
bam.file |
The complete file path to a bam file. |
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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