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, filter_depth = 10, 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).

filter_depth

Remove variants below this sequencing depth (integer).

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 1.4.1 Index]