prepareAnnoFile4affy: prepare Affymetrix chip annotation file

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

prepare Affymetrix chip annotation file

Description

Prepare Affymetrix chip annotation file into the format of interest.

Usage

prepareAnnoFile4affy(inputFile, outputFile, chipType)

Arguments

inputFile	an input pure text file that contains the chip annotation information.
outputFile	an output pure text file that stores the chip annotation information in a user-defined format.
chipType	a string name defines the type of the chip annotation file: 'SNPIDstudy', and 'rsIDstudy'.

Details

If the chip annotation file is not available for your study, it can be downloaded from http://www.well.ox.ac.uk/~wrayner/strand/. The chip annotation file is organized into two different types:

1. If the snp name of your study genotype data starts with "SNP_", then the chip type "SNPIDstudy" is used; Usually, Affymetrix chip data belongs to this category. The prepared output annotation file must at least consist of the following column names: SNPIDstudy, rs, chr, pos, strand.

2. If the snp name of your study genotype data starts with "rs", then the chip type "rsIDstudy" is used; The prepared output annotation file must at least consist of the following column names: SNPIDstudy, rs, chr, pos, strand. Illumina chip is often specified in this format.

The column "strand" must only have two kinds of values "-" and "+". Variants with all other values should be excluded.

Value

a pure text file that stores the prepared chip annotation information in a user-defined format.

Author(s)

Junfang Chen

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