reductExpand: Post imputation data extraction and expansion

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

Post imputation data extraction and expansion

Description

Reduce well imputed dataset to have SNPs before imputation and then added genotype data that are different from the imputation reference panel.

Usage

reductExpand(
  plink,
  referencePanel,
  inputPrefix,
  inputQCprefix,
  snpRefAlleleFile,
  snpDiffAlleleFile,
  snpMissPosFile,
  snpSameNameDifPosFile,
  reducedToSpecificfn,
  specificDiffAllelefn,
  specificMissPosfn,
  specificDiffPosfn
)

Arguments

plink	an executable program in either the current working directory or somewhere in the command path.
referencePanel	a string indicating the type of imputation reference panels is used: c("1000Gphase1v3_macGT1", "1000Gphase3").
inputPrefix	the prefix of final well imputed PLINK files.
inputQCprefix	the prefix of QCed PLINK files.
snpRefAlleleFile	the output plain text file that stores the removed SNPs whose alleles are in the imputation reference, taking their genomic positions into account.
snpDiffAlleleFile	the output plain text file that stores the removed SNPs whose alleles are not in the imputation reference, taking their genomic positions into account.
snpMissPosFile	the output plain text file that stores the removed SNPs whose genomic positions are not in the imputation reference, ingoring SNP names.
snpSameNameDifPosFile	the output plain text file that stores the removed SNPs whose genomic positions are not in the imputation reference, taking SNP names into account.
reducedToSpecificfn	the prefix of PLINK files which are reduced in the number of SNPs and contain only SNPs prior to imputation.
specificDiffAllelefn	the prefix of PLINK files which added genotypes with different alleles other than the imputation to the file with the prefix: reducedToSpecificfn.
specificMissPosfn	the prefix of PLINK files which added genotypes with missing positions other than the imputation to the file with the prefix: specificDiffAllelefn.
specificDiffPosfn	the prefix of PLINK files which added genotypes with different positions other than the imputation to the file with the prefix: specificMissPosfn .

Value

Extracted genotypes from the imputed data which contain SNPs before imputation. On the basis of extracted genotypes, genotypes different from the imputation reference panel are appended, including SNPs with different alleles, missing positions, and different positions.

Author(s)

Junfang Chen

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