removedDoubleProbes: Remove duplicated probes or SNPs

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

Description

Remove duplicated probes or SNPs that have same rs-names but different SNP-A IDs found in chip annotation information (only for Affymetrix chip). This chip annotation file is defined in the configuration folder.

Usage

removedDoubleProbes(plink, inputPrefix, chipAnnoFile, chipType,
  outputSNPdupFile, outputPrefix)

Arguments

plink	an executable PLINK program in either the current working directory or somewhere in the command path.
inputPrefix	the prefix of the input PLINK format files.
chipAnnoFile	a pure text file that stores the chip annotation information (Affymetrix, Illumination, PsychChip and so on). This file can be found http://www.well.ox.ac.uk/~wrayner/strand/.
chipType	a string name that defines the type of the chip annotation file: 'Illumina', 'affymetrix' or 'psychChip'.
outputSNPdupFile	a pure text file that stores the duplicated probe/SNP IDs, which can be found with the help of the chip annotation file.
outputPrefix	the prefix of the output PLINK format files.

Value

The output PLINK format files after removing duplicated probe IDs.

Author(s)

Junfang Chen <[e-mail]>

Junfang/Gimpute documentation built on May 17, 2019, 10:11 p.m.