ghap.loadphase {GHap}

Load binary phased genotype data

Description

This function loads binary phased genotype data and converts them into a native GHap.phase object.

Usage

  ghap.loadphase(input.file = NULL,
                 samples.file = NULL,
                 markers.file = NULL,
                 phaseb.file = NULL,
                 ncores = 1, verbose = TRUE)

Arguments

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

input.file

Prefix for input files.

For backward compatibility, the user can still point to input files separately:

samples.file

Individual information.

markers.file

Variant map information.

phaseb.file

Binary phased genotype matrix, such as supplied by the ghap.compress function.

To turn loading progress-tracking on or off, or use multiple cores, please use:

ncores

A numerical value specfying the number of cores to use while loading the input files (default = 1).

verbose

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

Value

The returned GHap.phase object is a list with components:

nsamples

An integer value for the sample size.

nmarkers

An integer value for the number of markers.

nsamples.in

An integer value for the number of active samples.

nmarkers.in

An integer value for the number of active markers.

pop

A character vector relating chromosome alleles to populations. This information is obtained from the first column of the sample file.

id

A character vector mapping chromosome alleles to samples. This information is obtained from the second column of the sample file.

id.in

A logical vector indicating active chromosome alleles. By default, all chromosomes are set to TRUE.

sire

A character vector indicating sire names, as provided in the third column of the sample file (optional).

dam

A character vector indicating dam names, as provided in the fourth column of the sample file (optional).

sex

A character vector indicating individual sex, as provided in the fifth column of the sample file (optional). Codes are converted as follows: 0 = NA, 1 = Male and 2 = Female.

chr

A character vector indicating chromosome identity for each marker.

marker

A character vector containing marker names. This information is obtained from the second column of the marker map file.

marker.in

A logical vector indicating active markers. By default, all markers are set to TRUE.

cm

A numeric vector with genetic positions for markers. This information is obtained from the third column of the marker map file if it contains 6 columns. Otherwise, if the map file contains only 5 columns, genetic positions are considered absent and approximated from physical positions (in this case assumed to be the third column) as 1 Mb ~ 1 cM.

bp

A numeric vector with marker positions. This information is obtained from the third column of the marker map file if it contains 5 columns, or from the fourth column if it contains 6 columns.

A0

A character vector with reference alleles. This information is obtained from the fourth column of the marker map file in case it contains 5 columns, or from the fifth column if it contains 6 columns.

A1

A character vector with alternative alleles. This information is obtained from the last column of the marker map file.

phase

A character value giving the pathway to the binary phased genotype matrix.

Author(s)

Yuri Tani Utsunomiya <[e-mail]>
Marco Milanesi <[e-mail]>

Examples

# #### DO NOT RUN IF NOT NECESSARY ###
# 
# # Copy the example data in the current working directory
# exfiles <- ghap.makefile(dataset = "example",
#                          format = "phase",
#                          verbose = TRUE)
# file.copy(from = exfiles, to = "./")
# 
# ### RUN ###
# 
# # Load data using prefix
# phase <- ghap.loadphase(input.file = "example")
# 
# # Load data using file names
# phase <- ghap.loadphase(samples.file = "example.samples",
#                         markers.file = "example.markers",
#                         phaseb.file = "example.phaseb")