Empop2variant: Get variants from an EMPOP file

In Ahhgust/MMDIT: Mitochondrial mixture project

Description

This function takes an empop file containing at least four (mandatory) columns (refer to https://empop.online/downloads for the emp file format) and returns a tibble with two columns - SampleID and Variant All individuals in the empop file must be single-source, with *no* heteroplasmies We recommend taking the major allele in the case of heteroplasmy.

Note: if an individual has no differences to the reference (rCRS) it is encoded as having a 73A. This is NOT a variant allele, but otherwise the tabular data format cannot easily represent the difference encoding (this has no effect on the string-based match statistics)

Usage

Empop2variant(empopFile, s = 1, ncol2skip = 3, guess_max = 100)

Arguments

empopFile	An EMPOP file (tab seperated)
s	a numeric argument that tells the function how many rows of data to skip while reading in EMPOP file
ncol2skip	number of columns to skip (starting from left) in the empop file default=3
guess_max	a number; passed to read_delim. Helps with fast reading of files... If no value is provided, the first line is ommited by default

Examples

## Not run: 
  Empop2variant("EMPOP.emp")
  Empop2variant("EMPOP.emp", s = 3)

## End(Not run)

Ahhgust/MMDIT documentation built on Jan. 27, 2021, 11:48 a.m.