vcf.cov.ind: Calculate per-individual coverage from a vcf file
In spflanagan/gwscaR: Genome-wide Selection Components Analysis in R
Description
Usage
Arguments
Value
Description
Calculate per-individual coverage from a vcf file
Usage
1
vcf.cov.ind(vcf)
Arguments
vcf
A data.frame containing data in vcf format.
Value
A data.frame with one row for each individual and columns:
NumMissing: The number of missing loci
NumPresent: The number of loci genotyped in this individual
AvgCovRef: The average coverage for reference alleles across all genotyped loci in this individual
AvgCovAlt: The average coverage for alternative alleles across all genotyped loci in this individual
AvgCovTot: The average total coverage (ref + alt coverage) across all genotyped loci in this individual
PropHet: Proportion of loci at which this individual is heterozygous
NumReads: The total number of reads for this individual
spflanagan/gwscaR documentation built on Nov. 14, 2019, 9:16 p.m.
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Description Usage Arguments Value
Description
Calculate per-individual coverage from a vcf file
Usage
1 | vcf.cov.ind(vcf)
|
Arguments
vcf |
A data.frame containing data in vcf format. |
Value
A data.frame with one row for each individual and columns: NumMissing: The number of missing loci NumPresent: The number of loci genotyped in this individual AvgCovRef: The average coverage for reference alleles across all genotyped loci in this individual AvgCovAlt: The average coverage for alternative alleles across all genotyped loci in this individual AvgCovTot: The average total coverage (ref + alt coverage) across all genotyped loci in this individual PropHet: Proportion of loci at which this individual is heterozygous NumReads: The total number of reads for this individual
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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