postImpQC: Post imputation quality control

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

Post imputation quality control

Description

Perform quality control and data management after imputation.

Usage

postImpQC(
  plink,
  inputPrefix,
  out1,
  out2,
  out3,
  out4,
  outputInfoFile,
  infoScore = 0.6,
  outputMonoSNPfile,
  prefixAlign2ref,
  missCutoff = 20,
  outRemovedSNPfile,
  outRetainSNPfile,
  referencePanel
)

Arguments

plink	an executable program in either the current working directory or somewhere in the command path.
inputPrefix	the prefix of the final imputed PLINK files.
out1	the prefix of well imputed PLINK files with the index.
out2	the prefix of well imputed PLINK files after removing any SNPs with the same positions (if any), the index is also appended.
out3	the prefix of well imputed PLINK files with the index after adding previously identified monomorphic SNPs if any.
out4	the prefix of final well imputed PLINK files with the index.
outputInfoFile	the output file of impute2 info scores consisting of two columns: all imputed SNPs and their info scores.
infoScore	the cutoff of filtering imputation quality score for each variant. The default value is 0.6.
outputMonoSNPfile	the output pure text file that stores the removed monomorphic SNPs, one per line, if any.
prefixAlign2ref	the prefix of the output PLINK binary files after removing SNPs whose alleles are not in the imputation reference, taking their genomic positions into account.
missCutoff	the cutoff of the least number of instances for a SNP that is not missing. The default is 20.
outRemovedSNPfile	the output file of SNPs with pre-defined missing values that are removed.
outRetainSNPfile	the output file of SNPs that are retained.
referencePanel	a string indicating the type of imputation reference panels is used: c("1000Gphase1v3_macGT1", "1000Gphase3").

Value

All imputed genotype data in PLINK format, well imputed data and its variants, as well as a set of pure text files containing removed or retained SNPs.

Author(s)

Junfang Chen

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