computeInfoByQctool: Calculate the info score by QCTOOL

In transbioZI/Gimpute: Gimpute: An efficient genetic data processing and imputation pipeline

Calculate the info score by QCTOOL

Description

Calculate the info score by QCTOOL for a set of SNPs from .GEN files.

Usage

computeInfoByQctool(qctool, inputSuffix, outputInfoFile)

Arguments

qctool	an executable program in either the current working directory or somewhere in the command path.
inputSuffix	the suffix of input .GEN files within current directory.
outputInfoFile	the output info scores file consisting of two columns: all SNPs from .GEN files and their info scores.

Details

These .GEN files may come from the output of impute4 results. The intermediate generated files are retained in the directory.

Value

A pure text file contains the info scores of all SNPs from .GEN files with two columns: SNP names and the corresponding info scores.

Author(s)

Junfang Chen

Examples

## In the current working directory
inputSuffix <- "noINDEL.gen"
outputInfoFile <- "infoScore.txt"
## computeInfoByQctool(qctool, inputSuffix, outputInfoFile)

transbioZI/Gimpute documentation built on April 10, 2022, 4:20 a.m.