snpSummary: Counts and distribution statistics for SNPs in a VCF object
In Jiefei-Wang/VariantAnnotation: Annotation of Genetic Variants

Description Usage Arguments Details Value Author(s) See Also Examples

Counts and distribution statistics for SNPs in a VCF object

1 2	## S4 method for signature 'CollapsedVCF' snpSummary(x, ...)

`x`	A CollapsedVCF object.
`...`	Additional arguments to methods.

Genotype counts, allele counts and Hardy Weinberg equilibrium (HWE) statistics are calculated for single nucleotide variants in a CollapsedVCF object. HWE has been established as a useful quality filter on genotype data. This equilibrium should be attained in a single generation of random mating. Departures from HWE are indicated by small p values and are almost invariably indicative of a problem with genotype calls.

The following caveats apply:

No distinction is made between phased and unphased genotypes.
Only diploid calls are included.
Only ‘valid’ SNPs are included. A ‘valid’ SNP is defined as having a reference allele of length 1 and a single alternate allele of length 1.

Variants that do not meet these criteria are set to NA.

The object returned is a data.frame with seven columns.

g00: Counts for genotype 00 (homozygous reference).
g01: Counts for genotype 01 or 10 (heterozygous).
g11: Counts for genotype 11 (homozygous alternate).
a0Freq: Frequency of the reference allele.
a1Freq: Frequency of the alternate allele.
HWEzscore: Z-score for departure from a null hypothesis of Hardy Weinberg equilibrium.
HWEpvalue: p-value for departure from a null hypothesis of Hardy Weinberg equilibrium.

Chris Wallace <cew54@cam.ac.uk>

genotypeToSnpMatrix, probabilityToSnpMatrix

  fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")
  vcf <- readVcf(fl, "hg19")

  ## The return value is a data.frame with genotype counts
  ## and allele frequencies.
  df <- snpSummary(vcf)
  df

  ## Compare to ranges in the VCF object:
  rowRanges(vcf)

  ## No statistics were computed for the variants in rows 3, 4 
  ## and 5. They were omitted because row 3 has two alternate 
  ## alleles, row 4 has none and row 5 is not a SNP.