vcf.cov.loc: Calculate per-locus coverage from a vcf file
In spflanagan/gwscaR: Genome-wide Selection Components Analysis in R
Description
Usage
Arguments
Value
Description
Calculate per-locus coverage from a vcf file
Usage
1
vcf.cov.loc(vcf, subset = NULL)
Arguments
vcf
A data.frame containing data in vcf format.
subset
A list of the column names of the individuals to be used (optional)
Value
A data.frame with one row for each locus and 14 columns:
Chrom: The chromosome
Pos: The position/BP on the chromosome
Locus: The Locus ID
NumMissing: The number of individuals not gentoyped at this locus
NumPresent: The number of individuals genotyped at this locus
PropMissing: The proportion of individuals not genotyped at this locus
AvgCovRef: The average coverage of the reference allele in genotyped individuals
AvgCovAlt: The average coverage of the alternative allele in genotyped individuals
AvgCovRatio: The average ration of Reference/Alternative allele coverage
AvgCovTotal: The average of the number of reference + alternative reads per individual
CovVariance: The variance in coverage among individuals
NumHet: The number of individuals genotyped as heterozygotes
PropHet: The proportion of individuals genotyped as heterozygotes
TotalNumReads: The total number of reads at this locus
spflanagan/gwscaR documentation built on Nov. 14, 2019, 9:16 p.m.
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Description Usage Arguments Value
Description
Calculate per-locus coverage from a vcf file
Usage
1 | vcf.cov.loc(vcf, subset = NULL)
|
Arguments
vcf |
A data.frame containing data in vcf format. |
subset |
A list of the column names of the individuals to be used (optional) |
Value
A data.frame with one row for each locus and 14 columns: Chrom: The chromosome Pos: The position/BP on the chromosome Locus: The Locus ID NumMissing: The number of individuals not gentoyped at this locus NumPresent: The number of individuals genotyped at this locus PropMissing: The proportion of individuals not genotyped at this locus AvgCovRef: The average coverage of the reference allele in genotyped individuals AvgCovAlt: The average coverage of the alternative allele in genotyped individuals AvgCovRatio: The average ration of Reference/Alternative allele coverage AvgCovTotal: The average of the number of reference + alternative reads per individual CovVariance: The variance in coverage among individuals NumHet: The number of individuals genotyped as heterozygotes PropHet: The proportion of individuals genotyped as heterozygotes TotalNumReads: The total number of reads at this locus
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