oxford2phase: Convert Oxford data into GHap phase

In GHap: Genome-Wide Haplotyping

Convert Oxford data into GHap phase

Description

This function takes phased genotype data in Oxford HAPS/SAMPLES format and converts them into the GHap phase format.

Usage

  ghap.oxford2phase(input.files = NULL, haps.files = NULL,
                    sample.files = NULL, out.file,
                    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:

haps.files	Character vector containing the list of Oxford HAPS files.
sample.files	Character vector containing the list of Oxford SAMPLES files.

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

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

Details

The Oxford HAPS/SAMPLE format output of widely used phasing software such as SHAPEIT2 (O'Connell et al., 2014) or Eagle (Loh et al., 2106) is here manipulated to obtain the GHap phase format.

Author(s)

Mario Barbato <[e-mail]>, Yuri Tani Utsunomiya <[e-mail]>

References

R-R. Loh P-R et al. Reference-based phasing using the Haplotype Reference Consortium panel. Nat Genet. 2016. 48(11):1443-1448. J. O'Connell et al. A general approach for haplotype phasing across the full spectrum of relatedness. PLOS Genet. 2014. 10:e1004234.

See Also

ghap.compress, ghap.loadphase, ghap.fast2phase, ghap.vcf2phase

Examples

# #### DO NOT RUN IF NOT NECESSARY ###
# 
# # Copy the example data in the current working directory
# exfiles <- ghap.makefile(dataset = "example",
#                          format = "oxford",
#                          verbose = TRUE)
# file.copy(from = exfiles, to = "./")
# 
# ### RUN ###
# 
# # Convert from a single genome-wide file
# ghap.oxford2phase(input.files = "example",
#                   out.file = "example")
# 
# # Convert from a list of chromosome files
# ghap.oxford2phase(input.files = paste0("example_chr",1:10),
#                   out.file = "example")
# 
# # Convert using separate lists for file extensions
# ghap.oxford2phase(haps.files = paste0("example_chr",1:10,".haps"),
#                   sample.files = paste0("example_chr",1:10,".sample"),
#                   out.file = "example")
# 
# # A more efficient alternative for *nix system users
# # Note: replace "cat" by "zcat" if files are gzipped
# haps.files = paste("example_chr",1:10,".haps",sep="")
# command <- "tail -n+3 example_chr1.sample | cut -d' ' -f1,2 > example.samples"
# system(command)
# for(i in 1:10){
#   command <- paste("cat",haps.files[i],"| cut -d' ' -f1-5 >> example.markers")
#   system(command)
#   command <- paste("cat",haps.files[i],"| cut -d' ' -f1-5 --complement >> example.phase")
#   system(command)
# }

GHap documentation built on July 2, 2022, 1:07 a.m.