Description Slots Extends Methods Author(s)

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.

`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.

Class `"countData"`

, directly.

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

Thomas J. Hardcastle

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