vcf2diem {diemr}

Convert vcf files to diem format

Description

Reads vcf files and writes genotypes of the most frequent alleles based on chromosome positions to diem format.

Usage

vcf2diem(SNP, filename, chunk = 1L, ...)

Arguments

SNP

character vector with a path to the '.vcf' or '.vcf.gz' file, or an vcfR object. Diploid data are currently supported.

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. chunk = 1 saves all markers into one file.

...

additional arguments.

Details

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.

Value

No value returned, called for side effects.

Examples

## 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)