convert_plinkA: Convert PLINK recoded A to SNP file.

In stefanedwards/Siccuracy: Pipeline Package for AlphaImpute

Description

Facilitates converting a PLINK binary file to simplified SNP file format. Requires using PLINK to recode it to the A format by using command line plink -bfile <file stem> --recode A. This function then swiftly strips of first 6 columns (family ID, sample ID, paternal ID, maternal ID, sex, phenotypic record) and inserts an integer-based ID column. NA's outputted from PLINK are replaced with na argument.

Usage

convert_plinkA(rawfn, outfn, newID = 0, ncol = NULL, nlines = NULL,
  na = 9)

Arguments

rawfn	Plink output filename. Most likely plink.raw if PLINK command line argument --out is not used.
outfn	Filename of new file.
newID	Integer scalar (default 0) for automatically assigning new IDs. See description for more.
ncol	Integer,number of SNP columns in rawfn. When NULL, automagically detected with get_ncols(rawfn)-6.
nlines	Number of lines to process.
na	Missing value,

Value

Data.frame with columns famID, sampID, and newID.

Assigning new IDs

The new integer IDs can be supplied. If not, they will be made for you. newID may be an integer vector and will be used as is. If data.frame with columns famID, sampID, and newID, they will be reordered to match input file.

References

• PLINK. Purcell and Chang. https://www.cog-genomics.org/plink2

• Chang CC, Chow CC, Tellier LCAM, Vattikuti S, Purcell SM, Lee JJ (2015) Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience, 4. doi: 10.1186/s13742-015-0047-8 link.

See Also

convert_plink is a direct conversion that does not rely on PLINK.

stefanedwards/Siccuracy documentation built on May 30, 2019, 10:44 a.m.