lociData-class {segmentSeq} | R Documentation

## Class "lociData"

### Description

The `lociData` class is based on the `countData` class defined in the ‘baySeq’ package, but includes a ‘coordinates’ slot giving the coordinates of genomic loci and a ‘locLikelihoods’ slot which contains the estimated likelihoods that each annotated region is a locus in each replicate group and a coordinates structure giving the locations of the loci.

### Slots

`locLikelihoods`:

  Object of class `"matrix"` describing estimated likelihoods that each region defined in ‘coordinates’ is a locus in each replicate group.

`coordinates`:

  Object of class `"GRanges"` defining the coordinates of the genomic loci.

`data`:

  Object of class `"matrix"` defining count data for each locus defined in ‘coordinates’

`replicates`:

  Object of class `"factor"` defining the replicate structure of the data.

`groups`:

  Object of class `"list"` defing the group (model) structure of the data (see the `baySeq package`)

.

`annotation`:

  Object of class `"data.frame"` giving any additional annotation information for each locus.

`priorType`:

  Object of class `"character"` describing the type of prior information available in slot `'priors'`.

`priors`:

  Object of class `"list"` defing the prior parameter information. Calculated by the baySeq package.

`posteriors`:

  Object of class `"matrix"` giving the estimated posterior likelihoods for each replicate group. Calculated by the baySeq package.

`nullPosts`:

  Object of class `"numeric"` which, if calculated, defines the posterior likelihoods for the data having no true expression of any kind. Calculated by the baySeq package.

`estProps`:

  Object of class `"numeric"` giving the estimated proportion of tags belonnging to each group. Calculated by the baySeq package.

`cellObservables`

  A list object containing arrays of identical dimension to that in the ‘@data’ slot. These arrays define some observed characteristic of the data (e.g., GC content of sRNAs) which may be used in analysis.

`rowObservables`

  A list object containing arrays with first dimension identical to the number of rows in the ‘@data’ slot. These arrays define some observed characteristic of the data (e.g., genomic length of the region) which may be used in analysis.

`sampleObservables`

  A list object containing arrays with first dimension identical to the number of columns of the ‘@data’ slot. These arrays define some observed characteristic of the data (e.g., library scaling factor) which may be used in analysis.

### Extends

Class `"countData"`, directly.

### Methods

Methods ‘new’, ‘dim’, ‘[’, ‘c’ and ‘show’ have been defined for this class.

### Author(s)

Thomas J. Hardcastle

[Package segmentSeq version 2.24.0 Index]