freq_estimate: Estimation of frequencies of clones identified by 'alphabetr'
In alphabetr: Algorithms for High-Throughput Sequencing of Antigen-Specific T Cells

Description Usage Arguments Value Examples

freq_estimate() estimates the frequencies of clones with confidence intervals by using a maximum likelihood approach. The function looks at the wells that a chains of a clone appear in and determines the most likely frequency that explains the data.

1	freq_estimate(alpha, beta, pair, error = 0.15, numb_cells)

`alpha`	Matrix recording which alpha chains appear in each well of the data. See `create_data`.
`beta`	Matrix recording which beta chains appear in the each well of the data. See `create_data`.
`pair`	A matrix where each row is a beta/alpha pair, column 1 and 2 are the beta indices, and column 3 and 4 are the alpha indices, and column 5 is the proportion of replicates the clone was found in (or equal to -1 if the clone is dual)
`error`	The mean error "dropped" chain rate due to PCR or sequencing errors.
`numb_cells`	The number of cells per well in each column of the plates. Should be a vector of 12 elements.

A data frame with frequency estimates and confidence intervals

 ## Not run: 
 # obtained from the output of bagpipe()
 pairs <- pairs[pairs[, 5] > 0.3, ]
 freq  <- freq_estimate(alpha = dat$alpha,
                        beta = dat$beta,
                        pair = pairs,
                        numb_cells = matrix(c(50, 480), ncol = 2))
 
## End(Not run)