ghap.loadhaplo | R Documentation |
This function loads HapGenotypes generated by ghap.haplotyping
and converts them to a native GHap.haplo object.
ghap.loadhaplo(input.file = NULL, hapsamples.file = NULL, hapalleles.file = NULL, hapgenotypesb.file = NULL, verbose = TRUE)
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). |
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
.
Yuri Tani Utsunomiya <ytutsunomiya@gmail.com>
Marco Milanesi <marco.milanesi.mm@gmail.com>
# #### 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")
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