extractCoverageFromTxt: Extract read counts from plain text file

In DEploid: Deconvolute Mixed Genomes with Unknown Proportions

Description

Extract read counts from tab-delimited text files of a single sample.

Usage

extractCoverageFromTxt(refFileName, altFileName)

Arguments

refFileName	Path of the reference allele count file.
altFileName	Path of the alternative allele count file.

Value

A data.frame contains four columns: chromosomes, positions, reference allele count, alternative allele count.

Note

The allele count files must be tab-delimited. The allele count files contain three columns: chromosomes, positions and allele count.

Examples

refFile = system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
altFile = system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
PG0390 = extractCoverageFromTxt(refFile, altFile)

DEploid documentation built on April 22, 2020, 1:04 a.m.