create_profiles {seqCAT} | R Documentation |
Create SNV profiles from all VCF files in a directory
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)
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). |
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.
A list of data frames.
# 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)