freq_estimate {alphabetr} | R Documentation |

## Estimation of frequencies of clones identified by `alphabetr`

### Description

`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.

### Usage

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

### Arguments

`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. |

### Value

A data frame with frequency estimates and confidence intervals

### Examples

```
## 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)
```

*alphabetr*version 0.2.2 Index]