plinkify: Create a pointer to a PLINK fileset

In andrewparkermorgan/argyle: Basic interface and QC for genotypes from Illumina Infinium arrays

Description

Create a pointer to a PLINK fileset

Usage

plinkify(gty, where = tempdir(), prefix = "stuff", flags = "", ...)

Arguments

gty	a length-1 character vector containing the path to an existing PLINK fileset, OR a genotypes object which will be converted to one
where	if gty, directory in which to write the new PLINK fileset
prefix	basename of the fileset to be created
flags	(ignored)
...	ignored

Details

Command-line PLINK takes its input from filesets on disk. This function creates a pointer to such a fileset after checking that all its members (*.bed, *.bim, *.fam) are present. Wrapper functions for various PLINK analyses accept this pointer as input.

When the fileset alraedy exists, an additional attribute ("where") is added to the result specifying where to place the output of any future PLINK calls. By default such files are routed to the temporary directory corresponding to the current R session, to avoid cluttering the directory containing the source fileset.

When the fileset does not exist and gty is a genotypes object, a new fileset is created in the location specified by where via a call to write.plink(gty). Then the path to that fileset is returned.

Value

a length-1 character vector with path to a PLINK binary fileset, of class "plink"

andrewparkermorgan/argyle documentation built on May 10, 2019, 11:08 a.m.