methData-class: Class "methData"

In segmentSeq: Methods for identifying small RNA loci from high-throughput sequencing data

Description

The methData 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 the number of methylated cytosines observed for each locus defined in ‘coordinates’

data:

Object of class "matrix" defining the number of un-methylated cytosines observed 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., nonconversion rates) which may be used in analysis.

Extends

Class "countData", directly.

Methods

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

Author(s)

Thomas J. Hardcastle

segmentSeq documentation built on Nov. 8, 2020, 5:18 p.m.