eXtensions to BioConductor's SummarizedExperiment framework, as proposed http://thread.gmane.org/gmane.science.biology.informatics.conductor/52971

xSummarizedExperiment.R

subset.SummarizedExperiment<-function(x
                                      ,rowSubset=TRUE
                                      ,colSubset=TRUE
                                      ,assaySubset=TRUE
                                      ,drop=FALSE
                                      ,provenanceTrack=FALSE
                                      ,...) {
    ## PURPOSE: implement subsetting of SummarizedExperiments by
    ##   rowSubset : expression in terms of the GRanges attributes (and
    ##               its mcols meta-data) held in rowData
    ##   colSubset : expression over the experimental meta-data held in
    ##               the colData DataFrame
    ##   assaySubset : character vector of the names of assays to be selected
    ##  provenanceTrack : control whether the text of the subsetting
    ##                    should be noted in the exptData
    ## AUTHOR: [email protected]
    x<-x[
         eval(as.expression(substitute(rowSubset)),as.data.frame(rowData(x)),.GlobalEnv)
         ,eval(as.expression(substitute(colSubset)),colData(x),.GlobalEnv)
         ,drop=drop,...]
    if (! identical(TRUE,assaySubset)) assays(x)<-assays(x)[assaySubset]
    if(provenanceTrack) {
        exptData(x)$rowSubset<-c(exptData(x)$rowSubset,as.character(substitute(rowSubset)))
        exptData(x)$colSubset<-c(exptData(x)$colSubset,as.character(substitute(colSubset)))
        exptData(x)$assaySubset<-c(exptData(x)$assaySubset,as.character(substitute(assaySubset)))
    }
    x
}
attr(subset,'ex')<-function() {
    example(SummarizedExperiment)
    assays(se1)$a2<-assays(se1)$counts*2
    assays(se1)$a3<-assays(se1)$counts*3
    benchmark(replications=100
              ,se1.ss1<-se1[start(rowData(se1))==344757,se1$Treatment=='ChIP']
              ,se1.ss2<-subset(se1,start==344757,Treatment=='ChIP')
              )
    stopifnot(identical(assays(se1.ss1),assays(se1.ss2)))
    se1.ss3<-subset(se1,strand=='+',Treatment=='ChIP',c('a2','a3'))
    stopifnot(identical(c('a2','a3'),names(assays(se1.ss3))))
}