R/0classes.R

In flagme: Analysis of Metabolomics GC/MS Data

setClass("peaksDataset",
         ## components of a GCMS dataset
         representation(rawdata="list", rawrt="list", mz="numeric", files="character",
                        peaksdata="list", peaksrt="list",
                        peaksind="list", peaksind.start="list",
                        peaksind.end="list") 
         )

setClassUnion("eitherMatrix", c("matrix", "matrix.csc"))

setClass("peaksAlignment",
         ## components of a pairwise alignment
         representation(v="list", r="eitherMatrix", sim="numeric",
                        gap="numeric", dist="numeric", D="numeric",
                        compressed="logical") 
         )

setGeneric("compress", function(object, verbose=TRUE, ...) standardGeneric("compress"))
setGeneric("decompress", function(object, verbose=TRUE, ...) standardGeneric("decompress"))
setGeneric("plotImage",
           function(object, run=1, rtrange=c(11,13), main=NULL,
                    mzrange=c(50,200), SCALE=log2, ...)
    standardGeneric("plotImage"))  

setClass("clusterAlignment",
         representation(runs="integer", aligned="matrix",
         gap="numeric", D="numeric", dist="matrix", alignments="list",
         merge="matrix")
         )

setClass("progressiveAlignment",
         ## components of a progressive Alignment (cluster tree used to guide alignment)
         representation(merges="list")
         )

setClass("betweenAlignment",
         representation(mergedPeaksDataset="peaksDataset",
         ind="matrix", imputeind="list", runs="integer",
         groups="character", cA="clusterAlignment",
         pA="progressiveAlignment", filtind="list", newind="list")
         )

setClass("multipleAlignment",
## alignment of several samples, possibly with multiple groups
representation(clusterAlignmentList="list",
               progressiveAlignmentList="list", timeDiff="list",
               impute="list", betweenAlignment="betweenAlignment")
)


## setClass(Class='correlationAlignment',
##          slots=c(Alignment='data.frame', Center='character'))