methData-class: Class "methData"
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.