README.md

snpTools

My R package for general tasks when working with SNP array data

Table of Contents

  1. Summary of tools
  2. Installation
  3. Example

Summary of tools

Currently, snpTools contains:

Installation

To install and attach snpTools, from within the R interpreter use:

devtools::install_github("funkhou9/snpTools")
library(snpTools)

This assumes you have the devtools package installed. If not, use install.packages("devtools") to install devtools from CRAN.

For more information on any particular function, use:

?fimpute_run

Example

fimpute_run() can be used to phase genotypes, given a genotyping dataset and SNP map with:

fimpute_run(geno = <geno>,
            map = <map>,
            path = "/path/to/FImpute",
            exclude_chr = "1 2 3 4 5 6 7 9 10 11 12 13 14 15 16 17 18 19 20 21")

The above code will invoke FImpute, so you should see standard FImpute stdout:

.--------------------------------------. | .---.--.-- . | | | | _|_ | | |--- | .--.--. .,-. . . | .-. | | | | | | | | )| | | (.-' | | ' --'--' ' `-|`-' `--`-`-'`--' | | | | | ' | | Version 2.2 | | | | Mehdi Sargolzaei, | | Jacques Chesnais and Flavio Schenkel | | Semex Alliance, ON | | CGIL, University of Guelph, ON | | | | Last update: Jan 16, 2014 | `--------------------------------------'



funkhou9/snpTools documentation built on May 16, 2019, 4:05 p.m.