set_gt_conc: Cell-distribution variability upon phasing

In edsgard/scphaser: Phase Variants Within Genes Using Allele Counts

Description

set_gt_conc calculates an approximate measure of the spread of the cells in the allele-specific expression variant-space per gene

Usage

set_gt_conc(acset)

Arguments

acset

An acset list created by new_acset. The acset must contain an element 'gt', see call_gt and an element 'gt_phased', see function phase.

Details

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.

Value

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).

Examples

##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)

edsgard/scphaser documentation built on May 15, 2019, 11:02 p.m.