removedSnpMissDiff: Remove SNPs with difference in SNP missingness between cases...
In Junfang/Gimpute: Gimpute: An efficient genetic data processing and imputation pipeline
Description
Usage
Arguments
Value
Author(s)
Description
Remove SNPs with difference in SNP missingness between cases and controls.
To test for differential call rates between cases and controls for each SNP
This only works for the genotype data set with cases and controls.
Usage
1
2
removedSnpMissDiff(plink, inputPrefix, snpMissDifCutOff, outputPrefix,
caseControl)
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.
snpMissDifCutOff
the cutoff of the difference in missingness between cases and controls.
outputPrefix
the prefix of the output PLINK format files.
caseControl
a logical value indicating whether the data set contains both case-control subjects.
Value
The output PLINK format files.
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 SNPs with difference in SNP missingness between cases and controls. To test for differential call rates between cases and controls for each SNP This only works for the genotype data set with cases and controls.
Usage
1 2 | removedSnpMissDiff(plink, inputPrefix, snpMissDifCutOff, outputPrefix,
caseControl)
|
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. |
snpMissDifCutOff |
the cutoff of the difference in missingness between cases and controls. |
outputPrefix |
the prefix of the output PLINK format files. |
caseControl |
a logical value indicating whether the data set contains both case-control subjects. |
Value
The output PLINK format files.
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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