ghap.loadhaplo {GHap} | R Documentation |
Load haplotype genotype data
Description
This function loads HapGenotypes generated by ghap.haplotyping
and converts them to a native GHap.haplo object.
Usage
ghap.loadhaplo(input.file = NULL,
hapsamples.file = NULL,
hapalleles.file = NULL,
hapgenotypesb.file = NULL,
verbose = TRUE)
Arguments
input.file |
Prefix for input files. |
hapsamples.file |
Individual information file. |
hapalleles.file |
Haplotype alleles information file. |
hapgenotypesb.file |
Binary haplotype genotype matrix file. |
verbose |
A logical value specifying whether log messages should be printed (default = TRUE). |
Value
The returned GHap.haplo object is a list with components:
nsamples |
An integer value for the sample size. |
nalleles |
An integer value for the number of haplotype alleles. |
nsamples.in |
An integer value for the number of active samples. |
nalleles.in |
An integer value for the number of active haplotype alleles. |
pop |
A character vector relating samples to populations. This information is obtained from the first column of the hapsamples file. |
id |
A character vector mapping genotypes to samples. This information is obtained from the second column of the hapsamples file. |
id.in |
A logical vector indicating active samples. By default, all samples are set to TRUE. |
chr |
A character vector mapping haplotype alleles to chromosomes. This information is obtained from the second column of the hapalleles file. |
block |
A character vector containing block names. This information is obtained from the first column of the hapalleles file. |
bp1 |
A numeric vector with haplotype allele start positions. This information is obtained from the third column of the hapalleles file. |
bp2 |
A numeric vector with haplotype allele end positions. This information is obtained from the fourth column of the hapalleles file. |
allele |
A character vector with haplotype allele identity. This information is obtained from the fifth column of the hapalleles file. |
allele.in |
A logical vector indicating active haplotype alleles. By default, all alleles are set to TRUE. |
genotypes |
A character value giving the pathway to the binary haplotype genotype matrix. |
The input format is described in ghap.haplotyping
.
Author(s)
Yuri Tani Utsunomiya <ytutsunomiya@gmail.com>
Marco Milanesi <marco.milanesi.mm@gmail.com>
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")
#
# # Generate blocks of 5 markers sliding 5 markers at a time
# blocks <- ghap.blockgen(phase, windowsize = 5,
# slide = 5, unit = "marker")
#
# # Haplotyping
# ghap.haplotyping(phase = phase, blocks = blocks, outfile = "example",
# binary = T, ncores = 1)
#
# ### RUN ###
#
# # Load haplotype genotypes using prefix
# haplo <- ghap.loadhaplo("example")
#
# # Load haplotype genotypes using file names
# haplo <- ghap.loadhaplo(hapsamples.file = "example.hapsamples",
# hapalleles.file = "example.hapalleles",
# hapgenotypesb.file = "example.hapgenotypesb")