| vcf2diem {diemr} | R Documentation |
Reads vcf files and writes genotypes of the most frequent alleles based on chromosome positions to diem format.
vcf2diem(SNP, filename, chunk = 1L, ...)
SNP |
character vector with a path to the '.vcf' or '.vcf.gz' file, or an |
filename |
character vector with a path where to save the converted genotypes. |
chunk |
numeric indicating by how many markers should the result be split into
separate files. |
... |
additional arguments. |
Importing vcf files larger than 1GB is not recommended. The path to the
vcf file in SNP reads the file line by line, and might be a solution for
very large genomic datasets.
The number of files \code{vcf2diem} creates depends on the \code{chunk} argument
and class of the \code{SNP} object.
* When \code{chunk = 1}, one output file will be created.
* Values of \code{chunk < 100} are interpreted as the number of files into which to
split data in \code{SNP}. For \code{SNP} object of class \code{vcfR}, the number
of markers per file is calculated from the dimensions of \code{SNP}. When class
of \code{SNP} is \code{character}, the number of markers per file is approximated
from a model with a message. If this number is inappropriate for the expected
output, provide the intended number of markers per file in \code{chunk} greater
than 100. \code{vcf2diem} will scan the whole input \code{SNP} file, creating
additional output files until the last line in \code{SNP} is reached.
* Values of \code{chunk >= 100} mean that each output file
in diem format will contain \code{chunk} number of lines with the data in \code{SNP}.
When the vcf file contains markers non-informative for genome polarisation, those
those are removed and listed in a file *omittedLoci.txt* in the working directory.
The omitted loci are identified by their information in the CHROM and POS columns.
No value returned, called for side effects.
## Not run:
# vcf2diem will write files to a working directory or a specified folder
# make sure the working directory or the folder are at a location with write permission
myofile <- system.file("extdata", "myotis.vcf", package = "diemr")
myovcf <- vcfR::read.vcfR(myofile)
vcf2diem(SNP = myofile, filename = "test1")
vcf2diem(SNP = myofile, filename = "test2", chunk = 3)
vcf2diem(SNP = myovcf, filename = "test3")
vcf2diem(SNP = myovcf, filename = "test4", chunk = 3)
## End(Not run)