computeCoverage {Genominator} | R Documentation

## Compute effort-coverage values

### Description

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

### Usage

    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 `ExpData` object.
`annoData` | A data frame which must contain the columns `chr`, `start`, `end` and `strand` which specifies annotation regions of interest.
`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

    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)

[Package Genominator version 1.40.0 Index]