checkAlign2ref: Check the alignment with the imputation reference panel

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

Check the alignment with the imputation reference panel

Description

Perform the alignment against a reference panel by considering the following parameters: variant name, genomic position and the allele profile. Output files are generated sequentially depending on their previous PLINK data.

Usage

checkAlign2ref(
  plink,
  inputPrefix,
  referencePanel,
  bimReferenceFile,
  out2,
  out2.snp,
  out3,
  out3.snp,
  out4,
  out4.snp,
  out4.snpRetained,
  nCore = 25
)

Arguments

plink	an executable program in either the current working directory or somewhere in the command path.
inputPrefix	the prefix of the input PLINK files.
referencePanel	a string indicating the type of imputation reference panels is used: c("1000Gphase1v3_macGT1", "1000Gphase3").
bimReferenceFile	the reference file used for the alignment, which is a PLINK BIM alike format file.
out2	the prefix of the output PLINK binary files after removing SNPs whose genomic positions are not in the imputation reference, taking SNP names into account.
out2.snp	the output plain text file that stores the removed SNPs whose genomic positions are not in the imputation reference, taking SNP names into account.
out3	the prefix of the output PLINK binary files after removing SNPs whose genomic positions are not in the imputation reference, ingoring SNP names.
out3.snp	the output plain text file that stores the removed SNPs whose genomic positions are not in the imputation reference, ingoring SNP names.
out4	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.
out4.snp	the output plain text file that stores the removed SNPs whose alleles are not in the imputation reference, taking their genomic positions into account.
out4.snpRetained	the output plain text file that stores the removed SNPs whose alleles are in the imputation reference, taking their genomic positions into account.
nCore	the number of cores used for computation. This can be tuned along with nThread.

Details

The output files are genrated in order. Genomic position includes chromosomal location and base-pair position of the individual variant. All monomorphic SNPs are retained for further processing.

Value

The set of aligned PLINK files from your own study compared with the imputation reference.

Author(s)

Junfang Chen

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