ldstart: Create required (sub)directories for LD analysis

In cmcouto-silva/LD: Linkage Disequilibrium Analysis

Description

This function creates directories and subdirectories that will be used for accessing input files, as well as for delivering output files from LD analysis.

Usage

ldstart()

Details

Running this function generates the following folders at current directory: 'haplotypes', 'populations', 'snps', 'rehh_in', and 'rehh_out'. Users must place their data inside the respective directories, as explained below:

'haplotypes': The whole dataset of haplotypes (extensions .hap and .sample) split by chromosomes, obtained by Shapeit Software (http://www.shapeit.fr).

'populations': Text files from each population to be analyzed (one individual per line). File names must correspond to the names from populations (with or without ".txt" extension).

'snps': Text files with a set of SNP ID's (e.g. rs1042522), with or without ".txt" extension (a single ID per line).

Value

A set of required directories.

Examples

## Not run: ldstart() 

cmcouto-silva/LD documentation built on Sept. 20, 2020, 2:46 p.m.