add makeFeatureGRanges method for gSetList class
add elementLengths method for gSetList and faster ncol method. Bug fix for initialization methods
modify import directives from methods pkg
@<- has been moved from methods to base, so it no longer needs to
be imported in package NAMESPACEs.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligoClasses@72298 bc3139a8-67e5-0310-9ffc-ced21a209358
chromosome(gSetList) returns 'chr1'... format
add chromosome, isSnp, lrr, baf methods for SummarizedExperiment class
updates
change .getArm to only use markers that are <= start of the centromere gap or >= end of centromere gap
deprecated RangdDataCNV
Add SummarizedExperiment methods
update dependencies for annotation pkgs
merge with collab

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligoClasses@72703 bc3139a8-67e5-0310-9ffc-ced21a209358
update dependency

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligoClasses@72704 bc3139a8-67e5-0310-9ffc-ced21a209358