refPanelTools

This package provides a collection of various tools for reference panel datasets created for GAUSS R package.

Installation

You can install the development version of refPanelTools from GitHub with:

# install.packages("devtools")
devtools::install_github("statsleelab/refPanelTools")

Example

This is a basic example which shows you how to extract genotype information for a user-specified genomic region:

library(refPanelTools)
chr.num <- 14
start.bp <- 104000000
end.bp   <- 104200000
num.pops <- 29
ref.index.file <- "/33KG/33kg_index.gz"
ref.data.file <- "/33KG/33kg_geno.gz"

# extract genotype data of a user-specified genomic region 
data.output <- paste0("33kg_chr",chr.num,"_reg_geno")
extract_reg_data(chr.num, start.bp, end.bp, num.pops, 
                 ref.index.file, ref.data.file, 
                 data.output)