removedSnpMissDiff: Remove SNPs with difference in SNP missingness between cases...

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

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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.