extractCoverageFromVcf: Extract VCF information
In DEploid.utils: 'DEploid' Data Analysis and Results Interpretation
extractCoverageFromVcf R Documentation
Extract VCF information
Description
Extract VCF information
Usage
extractCoverageFromVcf(filename, samplename)
Arguments
filename
VCF file name.
samplename
Sample name
Value
A dataframe list with members of haplotypes, proportions and log likelihood of the MCMC chain.
-
CHROM SNP chromosomes.
-
POS SNP positions.
-
refCount reference allele count.
-
altCount alternative allele count.
See Also
-
extractCoverageFromVcf
-
extractCoverageFromTxt
Examples
vcfFile = system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid.utils")
vcf = extractCoverageFromVcf(vcfFile, "PG0390-C")
DEploid.utils documentation built on April 3, 2025, 9:58 p.m.
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| extractCoverageFromVcf | R Documentation |
Extract VCF information
Description
Extract VCF information
Usage
extractCoverageFromVcf(filename, samplename)
Arguments
filename |
VCF file name. |
samplename |
Sample name |
Value
A dataframe list with members of haplotypes, proportions and log likelihood of the MCMC chain.
-
CHROMSNP chromosomes. -
POSSNP positions. -
refCountreference allele count. -
altCountalternative allele count.
See Also
-
extractCoverageFromVcf -
extractCoverageFromTxt
Examples
vcfFile = system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid.utils")
vcf = extractCoverageFromVcf(vcfFile, "PG0390-C")
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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