read_profile {seqCAT} | R Documentation

## Read SNV profile

### Description

Read an SNV profile 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_1.profile.txt.gz",
                          package = "seqCAT")

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

[Package seqCAT version 1.4.1 Index]