set_gt_conc calculates an approximate measure of the spread of the
cells in the allele-specific expression variant-space per gene
An acset list created by
To assess the success of the phasing one can calculate the degree of variability remaining if all cells with haplotype 2 are set to haplotype 1. As a rough measure of this this function calculates the variability as the number of cells that differ from the inferred haplotype for every gene with two variants. The differing number of cells per gene we denote as the inconcordance and the number of cells with identical haplotype to the inferred haplotype as concordance. This can be understood by viewing each cell as a point in a transcribed genotype variant space, where each dimension is a variant (within a gene), with values in the transcribed genotype domain. The expression of the alleles within a gene from a single cell will then tend to cluster towards the haplotype state, and the remaining variability of the cells in that space after phasing can be used to measure how well the cells conform to the haplotype.
acset An acset list where two elements have been added or updated, 'gt_conc' and 'gt_phased_conc'. The elements contain the concordance and inconcordance for every gene before (gt_conc) and after phasing (gt_phased_conc).
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##load dataset invisible(marinov) acset = new_acset(featdata = marinov[['featdata']], refcount = marinov[['refcount']], altcount = marinov[['altcount']], phenodata = marinov[['phenodata']]) ##Call gt acset = call_gt(acset, min_acount = 3, fc = 3) ##Filter variants and genes acset = filter_acset(acset, nmincells = 5, nminvar = 2) ##Phase acset = phase(acset, input = 'gt', weigh = FALSE, method = 'exhaust') ##Get genotype concordance before and after phasing acset = set_gt_conc(acset)
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