midas_to_bimbam: Convert MIDAS merge output to BIMBAM input

In surh/HMVAR: Human Microbiome Variant Analysis in R

Description

Convert MIDAS merge output to BIMBAM input

Usage

midas_to_bimbam(midas_dir, map, outdir, focal_group = NULL, prefix = NULL)

Arguments

midas_dir	Directory where midas merge output for one genome is located. Must contain files snps_info.txt, snps_depth.txt and snps_freq.txt
map	Data frame or tibble that maps samples to groups. It must have columns 'sample' and 'ID'.
outdir	Directory where to store the results. It will be created if it does not exists already. If it exists, and files with the output file names exist, they will be overwriten.
focal_group	A character string with the group that is going to be compared against everything else. If NULL, then the function assumes that column group contains only two levels.
prefix	Prefix to append to all filenames.

Value

A list with elements filenames and Dat. The first element contains the relative paths to the three BIMBAM files, and the second contains tibbles with the data written to those files

surh/HMVAR documentation built on Aug. 18, 2021, 1:21 a.m.