create_profiles {seqCAT} | R Documentation

## SNV profile creation

### Description

Create SNV profiles from all VCF files in a directory

### Usage

    create_profiles(vcf_dir, min_depth = 10, filter_vc = TRUE,
      filter_mt = TRUE, filter_ns = TRUE, filter_gd = TRUE,
      filter_pd = FALSE, pattern = NULL, recursive = FALSE)

### Arguments

`vcf_dir` | The VCF directory from which the profiles will be created (path).
`min_depth` | Remove variants below this sequencing depth (integer).
`filter_vc` | Filter variants failing variant caller criteria (boolean).
`filter_mt` | Filter mitochondrial variants (boolean).
`filter_ns` | Filter non-standard chromosomes (boolean).
`filter_gd` | Filter duplicate variants at the gene-level (boolean).
`filter_pd` | Filter duplicate variants at the position-level (boolean).
`pattern` | Only create profiles for a subset of files corresponding to this pattern (character).
`recursive` | Find VCF files recursively in sub-directories as well (boolean).

### Details

This functions is a convenience-wrapper for the 'create_profile' function, which will create SNV profiles for each and every VCF file in the provided directory. The file naming scheme used is '<sample>.vcf' and will dictate the each profile's sample name.

### Value

A list of data frames.

### Examples

    # Path to the test VCF directory
    vcf_dir = system.file("extdata", package = "seqCAT")

    # Create SNV profiles
    profiles <- create_profiles(vcf_dir, pattern = "test", recursive = TRUE)

[Package seqCAT version 1.14.1 Index]