In mehararumilli/webgqt: Webserver for Variant Filtering using Genotype Query Tools (GQT)

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>")

library(webGQT)

Abstract

webGQT implements mendelian inheritance models to filter canidate disease-causing variants from large-scale genomic datasets stored in GQT index files.

Supported functionalities

• allows user to define pedigree file
• perform filtering by recessive, dominant, de novo inheritance models
• compare SNPs by allele frequencies between population groups
• perform case-control comparisons

Installation

To install the latest development version from GitHub:

install.packages("devtools")
devtools::install_github('arumds/webGQT')

Usage

We'll first load the package.

library("webGQT")

This package has two functions:

1. To launch the server from personal computer

# run_webgqt function to launch the server on personal computer
run_webgqt <- function(gqt_path)

For example, if gqt is installed at /usr/local/bin/gqt, then the argument is given as:

run_webgqt <- function(gqt_path = "/usr/local/gqt/bin/gqt")

1. A function to copy the installed package and dependencies to shiny package directory

copy_shiny_gqt_app(copy_to)

An example value to the argument:

copy_shiny_gqt_app(copy_to = '/srv/shiny-server/')

mehararumilli/webgqt documentation built on Feb. 12, 2020, 12:26 p.m.