removedUnmapProbes: Remove unmapped probes or SNPs
In Junfang/Gimpute: Gimpute: An efficient genetic data processing and imputation pipeline
Description
Usage
Arguments
Value
Author(s)
Description
Remove probes or SNPs that are not mapped to the chip annotation information. This chip annotation file is defined in the configuration folder.
Usage
1
2
removedUnmapProbes(plink, inputPrefix, chipAnnoFile, outputPrefix,
outputSNPunmapFile)
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/.
outputPrefix
the prefix of the output PLINK format files.
outputSNPunmapFile
a pure text file that stores the probe/SNP IDs, which are not mapped to the chip annotation file.
Value
The output PLINK format files after removing unmapped probe IDs.
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 probes or SNPs that are not mapped to the chip annotation information. This chip annotation file is defined in the configuration folder.
Usage
1 2 | removedUnmapProbes(plink, inputPrefix, chipAnnoFile, outputPrefix,
outputSNPunmapFile)
|
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/. |
outputPrefix |
the prefix of the output PLINK format files. |
outputSNPunmapFile |
a pure text file that stores the probe/SNP IDs, which are not mapped to the chip annotation file. |
Value
The output PLINK format files after removing unmapped probe IDs.
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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