removeCancerVariants: Remove cancer variants
In acc-bioinfo/TMBleR: Tumor Mutational Burden Quantification From Gene Panels And WES
Description
Usage
Arguments
Value
Author(s)
View source: R/removeCancerVariants.R
Description
This function removes from the vcf dataset those variants defined as pathogenic
(cancer) in COSMIC or truncating variants in tumor suppressor genes.
Usage
1
removeCancerVariants(vcf, assembly, tsList)
Arguments
vcf
a CollapsedVCF object containing variants
assembly
human genome assembly: hg19 or hg38
tsList
path to file containg list of tumor suppressors. If not
provided a list of 1217 tumor suppressors from the TSgene2 database
is used.
Value
Returns a data.frame object containing only those variants
which passed the filter
Author(s)
Laura Fancello
acc-bioinfo/TMBleR documentation built on Dec. 18, 2021, 10:21 p.m.
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Description Usage Arguments Value Author(s)
View source: R/removeCancerVariants.R
Description
This function removes from the vcf dataset those variants defined as pathogenic (cancer) in COSMIC or truncating variants in tumor suppressor genes.
Usage
1 | removeCancerVariants(vcf, assembly, tsList)
|
Arguments
vcf |
a |
assembly |
human genome assembly: hg19 or hg38 |
tsList |
path to file containg list of tumor suppressors. If not provided a list of 1217 tumor suppressors from the TSgene2 database is used. |
Value
Returns a data.frame object containing only those variants
which passed the filter
Author(s)
Laura Fancello
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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