create_profiles {seqCAT} | R Documentation

## SNV profile creation

### Description

Create SNV profiles from all VCF files in a directory

### Usage

    create_profiles(vcf_dir, output_dir = ".", pattern = NULL,
      recursive = FALSE, min_depth = 10, filter = TRUE, python = FALSE)

### Arguments

`vcf_dir` | The VCF directory from which the profiles will be created (path).
`output_dir` | The output directory to put the SNV profiles in (path).
`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).
`min_depth` | Remove variants below this sequencing depth (integer).
`filter` | Remove variants not passing filtering criteria (boolean).
`python` | Extract variants using Python instead of R (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 output profile filenames.

### Value

Does not return any data object, but outputs results to output_dir (to save computational time from having to repeatedly create profiles).

### Examples

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

    # Create SNV profiles
    ## Not run:
     create_profiles(vcf_dir, output_dir = "profiles")
     create_profiles(vcf_dir, output_dir = "profiles", pattern = "test")
     create_profiles(vcf_dir, output_dir = "profiles", recursive = TRUE)

    ## End(Not run)

[Package seqCAT version 1.6.3 Index]