vcf2diem: Convert vcf files to diem format

In diemr: Diagnostic Index Expectation Maximisation in R

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, requireHomozygous = TRUE)

Arguments

SNP	A character vector with a path to the '.vcf' or '.vcf.gz' file, or an vcfR object. Diploid data are currently supported.
filename	A 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.
requireHomozygous	Logical whether to require the marker to have at least one homozygous individual for each allele.

Details

Importing vcf files larger than 1GB, and those containing multiallelic genotypes is not recommended. Instead, use the path to the vcf file in SNP. vcf2diem then reads the file line by line, which is a preferred solution for data conversion, especially for very large and complex genomic datasets.

The number of files vcf2diem creates depends on the chunk argument and class of the SNP object.

• Values of chunk < 100 are interpreted as the number of files into which to split data in SNP. For SNP object of class vcfR, the number of markers per file is calculated from the dimensions of SNP. When class of SNP is character, the number of markers per file is approximated from a model with a message. If this number of markers per file is inappropriate for the expected output, provide the intended number of markers per file in chunk greater than 100 (values greater than 10000 are recommended for genomic data). vcf2diem will scan the whole input specified in the SNP file, creating additional output files until the last line in SNP is reached.

• Values of chunk >= 100 mean that each output file in diem format will contain chunk number of lines with the data in SNP.

When the vcf file contains markers not informative for genome polarisation, those are removed and listed in a file ending with omittedSites.txt in the directory specified in the SNP argument or in the working directory. The omitted loci are identified by their information in the CHROM and POS columns, and include the QUAL column data. The last column is an integer specifying the reason why the respective marker was omitted. The reasons why markers are not informative for genome polarisation using diem are:

1. Marker has fewer than 2 alleles representing substitutions.

2. Required homozygous individuals for the 2 most frequent alleles are not present (optional, controlled by the requireHomozygous argument).

3. The second most frequent allele is found only in one heterozygous individual.

4. Dataset is invariant for the most frequent allele.

5. Dataset is invariant for the allele listed as the first ALT in the vcf input.

The CHROM, POS, and QUAL information for loci included in the converted files are listed in the file ending with includedSites.txt. Additional columns show which allele is encoded as 0 in its homozygous state and which is encoded as 2.

Value

No value returned, called for side effects.

Author(s)

Natalia Martinkova

Filip Jagos [e-mail]

Jachym Postulka [e-mail]

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")

vcf2diem(SNP = myofile, filename = "test1")
vcf2diem(SNP = myofile, filename = "test2", chunk = 3)

## End(Not run)

diemr documentation built on Sept. 23, 2024, 5:10 p.m.