prep_manta_vcf2: Prepare Manta VCF for Perl Circos
In umccr/rock: Rocking R at UMCCR
Description
Usage
Arguments
Value
Examples
Description
Prepares a Manta VCF for display in a Perl circos plot.
Usage
1
prep_manta_vcf2(vcf, ...)
Arguments
vcf
Path to Manta VCF file. Can be compressed or not.
...
Additional arguments for prep_manta_vcf.
Value
A dataframe (tibble) with the following fields from the VCF:
chrom1: homo sapiens CHROM
pos1: POS | INFO/BPI_START
pos1b: POS | INFO/BPI_START
chrom2: CHROM (for mate2 if BND)
pos2: INFO/END | INFO/BPI_END (for mate1 if BND)
pos2b: INFO/END | INFO/BPI_END (for mate1 if BND)
col: link colour
Examples
1
2
vcf <- system.file("extdata", "HCC2218_manta.vcf", package = "pebbles")
prep_manta_vcf2(vcf)
umccr/rock documentation built on Oct. 11, 2020, 8:10 a.m.
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Description Usage Arguments Value Examples
Description
Prepares a Manta VCF for display in a Perl circos plot.
Usage
1 | prep_manta_vcf2(vcf, ...)
|
Arguments
vcf |
Path to Manta VCF file. Can be compressed or not. |
... |
Additional arguments for |
Value
A dataframe (tibble) with the following fields from the VCF:
chrom1: homo sapiens
CHROMpos1:
POS|INFO/BPI_STARTpos1b:
POS|INFO/BPI_STARTchrom2:
CHROM(for mate2 if BND)pos2:
INFO/END|INFO/BPI_END(for mate1 if BND)pos2b:
INFO/END|INFO/BPI_END(for mate1 if BND)col: link colour
Examples
1 2 | vcf <- system.file("extdata", "HCC2218_manta.vcf", package = "pebbles")
prep_manta_vcf2(vcf)
|
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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