breakpointgr2bedpe: Converting breakpoint GRanges to BEDPE-like dataframe
In d-cameron/StructuralVariantAnnotation: Variant annotations for structural variants
Description
Usage
Arguments
Details
Value
Examples
Description
Converting breakpoint GRanges to BEDPE-like dataframe
Usage
1
Arguments
gr
A GRanges object.
Details
breakpointgr2bedpe converts a breakpoint GRanges to a BEDPE-formatted
dataframe. The BEDPE format consists of two sets of genomic loci, optional
columns of name, score, strand1, strand2 and any user-defined fields.
See https://bedtools.readthedocs.io/en/latest/content/general-usage.html
for more details on the BEDPE format.
Value
A BEDPE-formatted data frame.
Examples
1
2
3
4
5
#coverting a GRanges object to BEDPE-like dataframe
vcf.file <- system.file("extdata", "gridss.vcf", package = "StructuralVariantAnnotation")
vcf <- VariantAnnotation::readVcf(vcf.file, "hg19")
gr <- breakpointRanges(vcf)
breakpointgr2bedpe(gr)
d-cameron/StructuralVariantAnnotation documentation built on Dec. 26, 2021, 6:14 p.m.
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Description Usage Arguments Details Value Examples
Description
Converting breakpoint GRanges to BEDPE-like dataframe
Usage
1 |
Arguments
gr |
A GRanges object. |
Details
breakpointgr2bedpe converts a breakpoint GRanges to a BEDPE-formatted
dataframe. The BEDPE format consists of two sets of genomic loci, optional
columns of name, score, strand1, strand2 and any user-defined fields.
See https://bedtools.readthedocs.io/en/latest/content/general-usage.html
for more details on the BEDPE format.
Value
A BEDPE-formatted data frame.
Examples
1 2 3 4 5 | #coverting a GRanges object to BEDPE-like dataframe
vcf.file <- system.file("extdata", "gridss.vcf", package = "StructuralVariantAnnotation")
vcf <- VariantAnnotation::readVcf(vcf.file, "hg19")
gr <- breakpointRanges(vcf)
breakpointgr2bedpe(gr)
|
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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