extract_variants_from_maf: Extract variants from a maf object
In musicatk: Mutational Signature Comprehensive Analysis Toolkit
Description
Usage
Arguments
Value
Examples
Description
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Usage
1
extract_variants_from_maf(maf, extra_fields = NULL)
Arguments
maf
MAF object loaded by read.maf() from the 'maftools' package
extra_fields
Optionally extract additional columns from the
maf object. Default NULL.
Value
Returns a data.table of variants from a maf which can be used to
create a musica object.
Examples
1
2
3
4
5
maf_file <- system.file("extdata", "public_TCGA.LUSC.maf",
package = "musicatk")
library(maftools)
maf <- read.maf(maf_file)
variants <- extract_variants_from_maf(maf = maf)
musicatk documentation built on Nov. 8, 2020, 5:16 p.m.
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Description Usage Arguments Value Examples
Description
Add description
Usage
1 | extract_variants_from_maf(maf, extra_fields = NULL)
|
Arguments
maf |
MAF object loaded by read.maf() from the 'maftools' package |
extra_fields |
Optionally extract additional columns from the
maf object. Default |
Value
Returns a data.table of variants from a maf which can be used to
create a musica object.
Examples
1 2 3 4 5 | maf_file <- system.file("extdata", "public_TCGA.LUSC.maf",
package = "musicatk")
library(maftools)
maf <- read.maf(maf_file)
variants <- extract_variants_from_maf(maf = maf)
|
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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