Upload_vcf_to_R: Turn vcf files to usable R files

In TomerAntman/VCFtoGWAS: Get GWAS out of VCF file

Turn vcf files to usable R files

Description

This function serves for step 1 of chapter 1 of the "Using VCFtoGWAS package" markdown series.
This script loads the vcf file that you want to work with (either processed by the "usegalaxy" server or not). The file can be uploaded in its zipped version (.gz file extension). The vcf processing is based on the [vcfR package](https://cran.r-project.org/web/packages/vcfR/vignettes/intro_to_vcfR.html).

Usage

Upload_vcf_to_R(vcf_file,
                dir_results = getwd(),
                results_name = name_by_time(),
                do_save = TRUE,
                do_return = TRUE,
                get_chr_info = TRUE,
                fix_columns = c("CHROM","POS","REF","ALT","QUAL"))

Arguments

vcf_file	The location where the vcf file is saved
dir_results	The directory in which a subfolder will be created and results will be saved. Make sure it exists!!!
results_name	The name of the folder in which the results will be saved within dir_results (default is a time stamp, see create_directory)
do_save	Do you wish to save the results? (will be saved as RDS files) (Default is TRUE)
do_return	Do you wish to return the results to your current workspace environment? (Default is TRUE)
get_chr_info	Information regarding the lengths of the chromosomes (Default is TRUE)
fix_columns	The column names that you wish to get from the fixed column of the vcf (the default is probably all you need so don't change it)

Details

These files are usually very large and it will take a while.
The files exported are saved as .RDS files. They are lighter and very easy to read in R by calling readRDS(file = filepath).

Extract genotypes from the vcf data:
GT: genotype, encoded as allele values separated by either of / or |.
The allele values are:

• 0 for the reference allele (what is in the REF field)

• 1 for the first allele listed in ALT

• 2 for the second allele listed in ALT.

• 3 for the third allele listed in ALT and so on.

For diploid calls examples could be 0/1, 1|0, or 1/2, etc. If a call cannot be made for a sample at a given locus, '.' is specified for each missing allele in the GT field (for example './.' for a diploid genotype and '.' for haploid genotype).
The meanings of the separators are as follows:

• / : genotype unphased

• | : genotype phased

Value

If do_return = TRUE:

fix_and_gt

is a list of two matrices: filtered fixed information (without unnecessary columns) and corresponding genotype section of the VCF

If do_return = FALSE:

results_directory

a string with the directory where the results were saved.

Note

Make sure you enter proper file routes (vcf_route) such as:

1) "somefolder/1011Matrix.gvcf.gz"
2) "Galaxy4_VCFselectsamples.vcf"

And also proper results route that exist (dir_results) such as:

1) "somefolder"
2) "C:/Users/user/Documents"

Author(s)

Tomer Antman

References

See vcfR package for more information

And also see the "usegalaxy" VCFselectsamples tool to pre-filter the data

Examples

files_directory <- Upload_vcf_to_R(
                                  vcf_file = "1011Matrix.gvcf.gz",
                                  dir_results = "C:/Users/user/Documents",
                                  do_return = FALSE
                                  )
print(files_directory)

TomerAntman/VCFtoGWAS documentation built on July 6, 2022, 4:51 a.m.