# Compute effort-coverage values

### Description

Compute fraction coverage obtained for a certain degree of sequencing effort.

### Usage

1 2 3 4 5 6 7 8 | ```
computeCoverage(expData, annoData,
cutoff = function(x, anno, group) { x > 10 },
effort = seq(1e+05, 5e+07, length = 20),
smooth = function(probs) { probs },
groups = rep("ALL", length(what)),
what = getColnames(expData, all = FALSE),
totals = summarizeExpData(expData, what = what, verbose = verbose),
ignoreStrand = FALSE, verbose = getOption("verbose"), ...)
``` |

### Arguments

`expData` |
An |

`annoData` |
A data frame which must contain the columns |

`cutoff` |
A predicate which determines when a region of annotation has been "sequenced". This function takes three arguments x = number of reads in region, anno = the annotation description of the region, group = the group it is in. |

`effort` |
Effort is a vector of how much sequencing has been done. |

`smooth` |
A function which takes as input the vector of probabilities and must return the probabilities. |

`groups` |
The different groups for which to calculate coverage. |

`what` |
The different columns, must be the same length as the groups. |

`totals` |
The lane totals, or some other totals. This allows us to estimate the sampling probability vector. |

`ignoreStrand` |
Whether or not to add over strands. |

`verbose` |
Do you want to see output. |

`...` |
Extra argument passed to cutoff. |

### Details

This argument is pretty general as different ways of specifying the arguments allows one to compute "coverage" under a lot of different definitions.

### Value

Returns an object of class `genominator.coverage`

. Pretty much
you'll want to call plot on this object.

### Author(s)

James Bullard bullard@berkeley.edu, Kasper Daniel Hansen khansen@jhsph.edu

### See Also

See the `plot.genominator.coverage`

for the plotting
method and the `Genominator`

vignette for details.

### Examples

1 2 3 4 5 6 | ```
ed <- ExpData(system.file(package = "Genominator", "sample.db"),
tablename = "raw")
data("yeastAnno")
a <- computeCoverage(ed, yeastAnno, effort = 2^(5:18),
cutoff = function(x, ...) x > 1, smooth = FALSE)
names(a)
``` |