chain_scores: Calculate association scores between alpha and beta chain...
In alphabetr: Algorithms for High-Throughput Sequencing of Antigen-Specific T Cells

Description Usage Arguments Value Examples

chain_scores() calculates association scores between every pair of alpha and beta chains based on the number of concurrent well appearances each alpha and beta pair makes, scaled inversely by the number of unique chains in that well. See Lee et. al. for more information about this procedure.

1	chain_scores(data_a, data_b)

`data_a`	Matrix recording which alpha chains appear in each well of the data. See `create_clones`.
`data_b`	Matrix recording which beta chains appear in the each well of the data. See `create_clones`.

A list containing the alpha and beta association scores. Accessed with list$ascores and list$bscores respectively.

 # see the help for create_clones() and create_data()
 clones <- create_clones(numb_beta = 1000,
                         dual_alpha = .3,
                         dual_beta  = .06,
                         alpha_sharing = c(0.80, 0.15, 0.05),
                         beta_sharing  = c(0.75, 0.20, 0.05))
 dat <- create_data(clones$TCR, plate = 5,
                    error_drop = c(.15, .01),
                    error_seq  = c(.05, .001),
                    error_mode = c("lognormal", "lognormal"),
                    skewed = 10,
                    prop_top = 0.6,
                    dist = "linear",
                    numb_cells = matrix(c(50, 480), ncol = 2))

 #this is done internally in bagpipe()
 scores <- chain_scores(data_a = dat$alpha, data_b = dat$beta)
 scores <- scores$ascores + t(scores$bscores)