extractVcf: Extract VCF information
In DEploid: Deconvolute Mixed Genomes with Unknown Proportions
Description
Usage
Arguments
Value
See Also
Examples
Description
Extract VCF information
Usage
1
extractVcf(filename)
Arguments
filename
VCF file 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
1
2
vcfFile = system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
vcf = extractVcf(vcfFile)
DEploid documentation built on April 22, 2020, 1:04 a.m.
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Description Usage Arguments Value See Also Examples
Description
Extract VCF information
Usage
1 | extractVcf(filename)
|
Arguments
filename |
VCF file 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
1 2 | vcfFile = system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
vcf = extractVcf(vcfFile)
|
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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