read_profile: Read SNV profile

Description Usage Arguments Details Value Examples

View source: R/read_profile.R

Description

Read an SNV profile for use in downstream comparisons.

Usage

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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

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# 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)

seqCAT documentation built on Nov. 1, 2018, 2:07 a.m.