create_profiles {seqCAT} | R Documentation |
Create SNV profiles from all VCF files in a directory
create_profiles(vcf_dir, output_dir = ".", pattern = NULL, recursive = FALSE, min_depth = 10, filter = TRUE, python = FALSE)
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). |
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.
Does not return any data object, but outputs results to output_dir (to save computational time from having to repeatedly create profiles).
# 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)