prep_manta_vcf: Prepare Manta VCF for Circos
In pdiakumis/rock: Rocking R at UMCCR
Description
Usage
Arguments
Value
Examples
Description
Prepares a Manta VCF for display in a Circos plot.
Usage
1
prep_manta_vcf(vcf, filter_pass = FALSE)
Arguments
vcf
Path to Manta VCF file. Can be compressed or not.
filter_pass
Keep only variants annotated with a PASS FILTER?
(default: FALSE).
Value
A dataframe (tibble) with the following fields from the VCF:
chrom1: CHROM
pos1: POS | INFO/BPI_START
chrom2: CHROM (for mate2 if BND)
pos2: INFO/END | INFO/BPI_END (for mate1 if BND)
svtype: INFO/SVTYPE. Used for plotting.
Examples
1
2
vcf <- system.file("extdata", "HCC2218_manta.vcf", package = "pebbles")
prep_manta_vcf(vcf)
pdiakumis/rock documentation built on Oct. 12, 2020, 9:38 a.m.
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Description Usage Arguments Value Examples
Description
Prepares a Manta VCF for display in a Circos plot.
Usage
1 | prep_manta_vcf(vcf, filter_pass = FALSE)
|
Arguments
vcf |
Path to Manta VCF file. Can be compressed or not. |
filter_pass |
Keep only variants annotated with a PASS FILTER? (default: FALSE). |
Value
A dataframe (tibble) with the following fields from the VCF:
chrom1:
CHROMpos1:
POS|INFO/BPI_STARTchrom2:
CHROM(for mate2 if BND)pos2:
INFO/END|INFO/BPI_END(for mate1 if BND)svtype:
INFO/SVTYPE. Used for plotting.
Examples
1 2 | vcf <- system.file("extdata", "HCC2218_manta.vcf", package = "pebbles")
prep_manta_vcf(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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