Algorithms for High-Throughput Sequencing of Antigen-Specific T Cells


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Documentation for package ‘alphabetr’ version 0.2.2

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bagpipe Identify candidate alpha/beta pairs.
chain_scores Calculate association scores between alpha and beta chain pairs.
combine_freq_results Combines the frequency estimation results from single TCR clones and dual TCR clones
create_clones Create a synthetic set of clones with a specific underlying clonal structure
create_data Simulate sequencing data obtained from the alphabetr approach with a specified clonal structure
create_data_singlecells Simulate sequencing data obtained single-cell sequencing
dual_discrim_dual_likelihood Calculate likelihood of two beta-sharing candidate alpha-beta pairs deriving from a dual clone
dual_discrim_shared_likelihood Calculate likelihood of two beta-sharing candidate alpha-beta pairs deriving from a dual clone
dual_eval Calculate dual depths and false dual rates for simulated alphabetr experiments
dual_tail Discriminate between beta-sharing clones and dual-alpha TCR clones (optimized for rare clones)
dual_top Discriminate between beta-sharing clones and dual-alpha TCR clones (optimized for common clones)
freq_estimate Estimation of frequencies of clones identified by 'alphabetr'
freq_eval Calculate the precision, CV, and accuracy of frequency estimates
likelihood_dual Calculate likelihood curve of frequency estimates for a dual-alpha or dual-beta TCR clone
likelihood_dualdual Calculate likelihood curve of frequency estimates for a dual-alpha and dual-beta TCR clone
likelihood_single Calculate likelihood curve of frequency estimates for a single TCR clone
read_alphabetr Read in alphabetr sequencing data into the binary matrix form needed by bagpipe()