create_profiles: SNV profile creation
In seqCAT: High Throughput Sequencing Cell Authentication Toolkit

Description Usage Arguments Details Value Examples

Create SNV profiles from all VCF files in a directory

1
2
3

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)