R: Convert fastPHASE data into the GHap phase format

ghap.fast2phase {GHap}

R Documentation

Convert fastPHASE data into the GHap phase format

Description

This function takes phased genotype data in fastPHASE format and converts them into a GHap plan and compressed binary format.

Usage

  ghap.fast2phase(input.files = NULL, switchout.files = NULL,
                  map.files = NULL, fam.file = NULL,
                  out.file = NULL, overwrite = FALSE,
                  ncores = 1, verbose = TRUE)

Arguments

If all input files share the same prefix, the user can use the following shortcut options:

`input.files`	Character vector with the list of prefixes for input files.
`out.file`	Character value for the output file name.

The user can also opt to point to input files separately:

`switchout.files`	Character vector containing the list of fastPHASE files.
`map.files`	Character vector containing the list of map files.
`fam.file`	Name of the file containing the population and individual ids.

The function avoids overwritting existing files by default. To change this behavior, please use:

overwrite

A logical value controling if existing files with the same name as the selected output should be overwritten (default = FALSE).

To turn conversion progress-tracking on or off or set the number of cores please use:

`ncores`	A numeric value specfying the number of cores (default = 1).
`verbose`	A logical value specfying whether log messages should be printed (default = TRUE).

Details

Currently this function handles _switch.out files from fastPHASE v1.4.0 or later. The map files should contain the following 5 space-delimited columns: chromosome, marker, position, allele 0 and allele 1 (no header). The fam file can have an arbitrary number of columns (with no header), but by default only the first two are read and should be space-delimited with the following data: population and individual name.

Author(s)

Mario Barbato <mario.barbato@unicatt.it>

References

Scheet, P., Stephens, M., 2006. A Fast and Flexible Statistical Model for Large-Scale Population Genotype Data: Applications to Inferring Missing Genotypes and Haplotypic Phase. Am. J. Hum. Genet. 78, 629-644. https://doi.org/10.1086/502802.