freq_estimate {alphabetr} | R Documentation |
alphabetr
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.
freq_estimate(alpha, beta, pair, error = 0.15, numb_cells)
alpha |
Matrix recording which alpha chains appear in each well of the
data. See |
beta |
Matrix recording which beta chains appear in the each well of the
data. See |
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)