CalcAlleleDiffs: Calculate allele differences

In wbooker/PloidyPal: Package for analysis of polyploid datasets

Description

This goes through individual text files for each specimen and calculates the distances between all alleles at a given locus or copy of that locus.

Usage

CalcAlleleDiffs("/CalcParamFile.csv")

Details

Parameter file should be a .csv with a header with four lines and two columns (see https://github.com/wbooker/PloidyPal for examples), names are in the left column and vlues in the right. rows are in order as follows: Begin number, end number, ploidy level, and root filepath.

Note

Files should be in this format:

—Individuals should be in seperate folders inside the root filepath with numbers followed by the letter I, as in 'I3756'

—Files should follow a similar format and be titled as thus: "I3756_allelesFromPost_4.txt"

—Each file should have alleles formatted thusly (see github for clear example):

>L1.1.1
AATTCCGGAA
>L1.1.2
AATTCGCCAA

Where the first number is the locus, second is the copy, and third is the allele number

Author(s)

William Booker Florida State University Dept. of Biological science

wbooker/PloidyPal documentation built on May 4, 2019, 2 a.m.