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 |

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

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

and `list$bscores`

respectively.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ```
# 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)
``` |

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