calculateVariantConcordance(gr1, gr2, which = NULL)
calculateConcordanceMatrix(variantFiles, ...)
callVariantConcordance(concordanceMatrix, threshold)GRanges to compareGRanges of positions to which the comparison is limited.
GRanges. Currently supports serialized (rda) and VCF files.
If the file extension is not “vcf”, we assume rda. Will be
improved in the future.
calculateConcordanceMatrix.
readVcf.calculateVariantConcordance, a
numeric matrix of concordances for calculateConcordanceMatrix,
or a character vector of status codes, named by sample, for
callVariantConcordance.
calculateVariantConcordance calculates the fraction of
concordant variants between two samples. Concordance is defined as
having the same position and alt allele. The calculateConcordanceMatrix function generates a numeric
matrix with the concordance for each pair of samples. It accepts paths
to serialized objects so that all variant calls are not loaded in
memory at once. This probably should support VCF files, eventually.
The callVariantConcordance function generates a
concordant/non-concordant/undecidable status for each sample (that are
assumed to originate from the same individual), given the output of
calculateConcordanceMatrix. The status is decided as follows. A
graph is formed from the concordance matrix using threshold to
generate the edges. If there are multiple cliques in the graph that
each have more than one sample, every sample is declared
undecidable. Otherwise, the samples in the clique with more than one
sample, if any, are marked as concordant, and the others (in singleton
cliques) are marked as discordant.