create_profile {seqCAT} | R Documentation

## SNV profile creation

### Description

Create an SNV profile from data in a VCF file.

### Usage

    create_profile(vcf_file, sample, min_depth = 10, filter_vc = TRUE,
      filter_mt = TRUE, filter_ns = TRUE, filter_gd = TRUE,
      filter_pd = FALSE)

### Arguments

`vcf_file` | The VCF file from which the profile will be created (path).
`sample` | The sample in the VCF for which a profile will be created (character).
`min_depth` | Filter 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).

### Details

This function creates a SNV profile from a given VCF file by extracting the variants that pass the filtering criterias. Profile creation is performed to facilitate and accelerate the cell authentication procedures, which is especially relevant when more than one pairwise comparison will be performed on the same sample.

### Value

A data frame.

### Examples

    # Path to the test VCF file
    vcf_file = system.file("extdata", "test.vcf.gz", package = "seqCAT")

    # Create SNV profiles
    profile_1 <- create_profile(vcf_file, "sample1")
    profile_1 <- create_profile(vcf_file, "sample1", min_depth = 15)

[Package seqCAT version 1.14.1 Index]