dot-prepareLegend2bim: Prepare a bim-like reference file

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

Prepare a bim-like reference file

Description

Prepare a bim-like file from the imputation reference legend file (e.g. 1000 genome project).

Usage

.prepareLegend2bim(inputFile, referencePanel, outputFile, ncore = 20)

Arguments

inputFile	a set of legend file from the imputation reference panel. For example, 1000 genome projects.
referencePanel	a string indicating the type of imputation reference panels is used: c("1000Gphase1v3_macGT1", "1000Gphase3").
outputFile	the pure text file that stores the prepared PLINK BIM file alike format data.
ncore	the number of cores used for computation. The default is 20.

Details

To prepare a bim-like reference file from legend files. One should first extract the specific content from these legend files after downloading. Note that extract only biallelic SNPs (only 1 allele in column3 and 4, and start with 'rs") and remove duplicated snp IDs. Column names are added in the end.

Value

Prepare a bim-like reference file. Note that the column names are already defined, i.e. "chr", "rsID", "pos", "a0", "a1."

Author(s)

Junfang Chen

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