ghap.phase2plink {GHap}

Export phase object to PLINK binary

Description

This function takes a phase object and converts it to the PLINK binary (bed/bim/fam) format.

Usage

ghap.phase2plink(object, out.file,
                 only.active.samples=TRUE,
                 only.active.markers=TRUE,
                 batchsize=NULL, ncores=1,
                 verbose=TRUE)

Arguments

object

A GHap.phase object.

out.file

A character value specifying the name used for the .bed, .bim and .fam output files.

only.active.samples

A logical value specifying whether only active samples should be included in the output (default = TRUE).

only.active.markers

A logical value specifying whether only active markers should be included in the output (default = TRUE).

batchsize

A numeric value controlling the number of markers to be processed and written to output at a time (default = nmarkers/10).

ncores

A numeric value specifying the number of cores to be used in parallel computations (default = 1).

verbose

A logical value specfying whether log messages should be printed (default = TRUE).

Details

The returned output is a standard set of PLINK (Purcell et al., 2007; Chang et al., 2015) binary file (bed/bim/fam), meaning that phase information will be lost during conversion.

Author(s)

Yuri Tani Utsunomiya <[e-mail]>

References

C. C. Chang et al. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience. 2015. 4, 7.

S. Purcell et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 2007. 81, 559-575.

Examples

# #### DO NOT RUN IF NOT NECESSARY ###
# 
# # Copy phase data in the current working directory
# exfiles <- ghap.makefile(dataset = "example",
#                          format = "phase",
#                          verbose = TRUE)
# file.copy(from = exfiles, to = "./")
# 
# # Load data
# phase <- ghap.loadphase("example")
# 
# ### RUN ###
# 
# # Convert to plink
# ghap.phase2plink(object = phase, out.file = "example")