updatedSnpInfo: Update the probes or SNPs information
In Junfang/Gimpute: Gimpute: An efficient genetic data processing and imputation pipeline
Description
Usage
Arguments
Value
Author(s)
Description
Remove SNP information including SNP name, genomic position, chromosome location and the strand information, with the help of the chip annotation file.
This chip annotation file is defined in the configuration folder.
Usage
1
updatedSnpInfo(plink, inputPrefix, chipAnnoFile, chipType, 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'.
outputPrefix
the prefix of the output PLINK format files.
Value
The output PLINK format files after updating SNP information.
Author(s)
Junfang Chen <junfang.chen3@gmail.com>
Junfang/Gimpute documentation built on May 17, 2019, 10:11 p.m.
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Description Usage Arguments Value Author(s)
Description
Remove SNP information including SNP name, genomic position, chromosome location and the strand information, with the help of the chip annotation file. This chip annotation file is defined in the configuration folder.
Usage
1 | updatedSnpInfo(plink, inputPrefix, chipAnnoFile, chipType, 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'. |
outputPrefix |
the prefix of the output PLINK format files. |
Value
The output PLINK format files after updating SNP information.
Author(s)
Junfang Chen <junfang.chen3@gmail.com>
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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