vcfs_to_maf_table: Read a VCF into an MAF-like table
In Townsend-Lab-Yale/cancereffectsizeR: Calculate Cancer Effect Size
View source: R/vcf_to_maf_table.R
vcfs_to_maf_table R Documentation
Read a VCF into an MAF-like table
Description
This function loads VCF files into MAF-like tables. A Tumor_Sample_Barcode column is
added, and the contents of the POS/REF/ALT fields are converted to match the style used
by MAF files for Start_Position/Reference_Allele/Tumor_Seq_Allele2. The VCF file
should represent high-confidence somatic variant calls for a single tumor sample.
Usage
vcfs_to_maf_table(vcfs, sample_ids)
Arguments
vcfs
Vector of VCF file paths, or a list of VCF-like data.tables, or a single data.table.
sample_ids
Identifiers to populate Tumor_Sample_Barcode, one per VCF.
Value
A single data.table with MAF-style fields, suitable for use with cancereffectsizeR.
Townsend-Lab-Yale/cancereffectsizeR documentation built on April 28, 2024, 6:14 p.m.
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.
View source: R/vcf_to_maf_table.R
| vcfs_to_maf_table | R Documentation |
Read a VCF into an MAF-like table
Description
This function loads VCF files into MAF-like tables. A Tumor_Sample_Barcode column is added, and the contents of the POS/REF/ALT fields are converted to match the style used by MAF files for Start_Position/Reference_Allele/Tumor_Seq_Allele2. The VCF file should represent high-confidence somatic variant calls for a single tumor sample.
Usage
vcfs_to_maf_table(vcfs, sample_ids)
Arguments
vcfs |
Vector of VCF file paths, or a list of VCF-like data.tables, or a single data.table. |
sample_ids |
Identifiers to populate Tumor_Sample_Barcode, one per VCF. |
Value
A single data.table with MAF-style fields, suitable for use with cancereffectsizeR.
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.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.