Add ... argument to assayDataNew in oligoSnpSet construction (allow for additional assay data elements)

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligoClasses@67364 bc3139a8-67e5-0310-9ffc-ced21a209358
update initialization method for oligoSnpSet

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligoClasses@67365 bc3139a8-67e5-0310-9ffc-ced21a209358
Do not require cnConfidence in oligoSnpSet object.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligoClasses@67366 bc3139a8-67e5-0310-9ffc-ced21a209358
Add function ADF2GDF for coercing AnnotatedDataFrame (ADF) to GenomeAnnotatedDataFrame (GDF)

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligoClasses@67367 bc3139a8-67e5-0310-9ffc-ced21a209358
bump description

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligoClasses@67368 bc3139a8-67e5-0310-9ffc-ced21a209358
Ability for GenomeAnnotatedDataFrame to have additional columns (e.g., chromosome arm).  Added unit test.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligoClasses@67369 bc3139a8-67e5-0310-9ffc-ced21a209358
UPdates to initialization method for GenomeAnnotatedDataFrame

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligoClasses@67370 bc3139a8-67e5-0310-9ffc-ced21a209358
Add methods-eSetList

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligoClasses@67371 bc3139a8-67e5-0310-9ffc-ced21a209358
Add AssayDataList constructor (moved from VI)

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligoClasses@67372 bc3139a8-67e5-0310-9ffc-ced21a209358
class of chromosome slot is vector (not integer)

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligoClasses@67373 bc3139a8-67e5-0310-9ffc-ced21a209358
Verify that assay data elements are integer matrices.  Update the news.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligoClasses@67374 bc3139a8-67e5-0310-9ffc-ced21a209358
unit tests use integer matrices

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligoClasses@67375 bc3139a8-67e5-0310-9ffc-ced21a209358
Add R/methods-eSetList and AssayDataList help file

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligoClasses@67376 bc3139a8-67e5-0310-9ffc-ced21a209358
update missing link in Rd file

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligoClasses@67377 bc3139a8-67e5-0310-9ffc-ced21a209358
update initialize method for BeadStudioSet -- remove checks for nrow(lrr) and nrow(baf)

checking the rows of lrr throws an error if assayData is provided instead

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligoClasses@67378 bc3139a8-67e5-0310-9ffc-ced21a209358
updates for GRanges classes

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligoClasses@67379 bc3139a8-67e5-0310-9ffc-ced21a209358
Add methods-GRangesHMM.R and methods-GRangesHMMList.R

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligoClasses@67380 bc3139a8-67e5-0310-9ffc-ced21a209358
commit test.rda

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligoClasses@67381 bc3139a8-67e5-0310-9ffc-ced21a209358
remove test.rda

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligoClasses@67382 bc3139a8-67e5-0310-9ffc-ced21a209358
SnpSet2 extends gSet. oligoSnpSet extends SnpSet2.  Require 'genome' slot in gSet derived classes.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligoClasses@67383 bc3139a8-67e5-0310-9ffc-ced21a209358