BinaryDosage (version 1.0.0)

getvcfinfo: Get information about a vcf file

Description

Routine to return information about a vcf file. This information is used by other routines to allow for quicker extraction of values from the file.

Usage

getvcfinfo(vcffiles, gz = FALSE, index = TRUE, snpidformat = 0L)

Arguments

vcffiles

A vector of file names. The first is the name of the vcf file. The second is name of the file that contains information about the imputation of the SNPs. This file is produced by minimac 3 and 4.

gz

Indicator if VCF file is compressed using gzip. Default value is FALSE.

index

Indicator if file should be indexed. This allows for faster reading of the file. Indexing a gzipped file is not supported. Default value is TRUE.

snpidformat

The format that the SNP ID will be saved as. 0 - same as in the VCF file 1 - chromosome:location 2 - chromosome:location:referenceallele:alternateallele If snpidformat is 1 and the VCF file uses format 2, an error is generated. Default value is 0.

Value

List containing information about the VCF file to include file name, subject IDs, and information about the SNPs. Indices for faster reading will be included if index is set to TRUE

Examples

# NOT RUN {
# Get file names of th vcf and infromation file
vcf1afile <- system.file("extdata", "set1a.vcf", package = "BinaryDosage")
vcf1ainfo <- system.file("extdata", "set1a.info", package = "BinaryDosage")

# Get the information about the vcf file
vcf1ainfo <- getvcfinfo(vcffiles = c(vcf1afile, vcf1ainfo))
# }