read_profile {seqCAT}R Documentation

Read SNV profile

Description

Read SNV profiles for use in downstream comparisons.

Usage

read_profile(file, sample_name, remove_mt = TRUE)

Arguments

file

The SNV profile to be read (path).

sample_name

The sample of the SNV profile (character).

remove_mt

Remove or keep mitochondrial variants (boolean).

Details

This is a function for reading SNV profiles created from VCF files. The data is returned as a GenomicRanges object, suitable for merging of metadata.

Value

A GRanges object.

Examples

# Path to test data
profile = system.file("extdata",
                      "test_profile_1.txt.gz",
                      package = "seqCAT")

# Read test profile
profile_1 <- read_profile(profile, "sample1")

[Package seqCAT version 1.2.1 Index]