Phase Variants Within Genes Using Allele Counts


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Documentation for package ‘scphaser’ version 1.0.0

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call_gt Call transcribed genotypes
filter_acset Filter variants and features
filter_feat_nminvar Filter features on minimal number of required variants
filter_homovars Filter homozygous variants
filter_var_gt Filter variants
filter_zerorow Filter variants with zero allele counts in all cells
marinov Single-cell RNA-seq allele counts for the Marinov et al dataset
mousehybrid Single-cell RNA-seq allele counts for a mouse-hybrid dataset
new_acset Construct an allele count set
phase Phasing of alleles
plot_conc Phasing concordance plot
racset Randomize an acset
set_gt_conc Cell-distribution variability upon phasing
subset_cols Subset cells
subset_feat Subset features
subset_rows Subset variants