Package: crlmm
Type: Package
Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
Version: 1.17.9
Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
License: Artistic-2.0
Depends: R (>= 2.14.0), oligoClasses (>= 1.19.39), preprocessCore (>= 1.17.7)
LinkingTo: preprocessCore (>= 1.17.7)
Imports: methods,
         Biobase (>= 2.15.4),
         BiocGenerics,
         affyio (>= 1.23.2),
         ellipse,
         genefilter (>= 1.37.1),
         mvtnorm,
         splines,
         stats,
         SNPchip,
         utils,
	 lattice,
	 ff,
	 foreach,
         RcppEigen
Suggests: hapmapsnp6,
          genomewidesnp6Crlmm (>= 1.0.4),
          GGdata,
          snpStats,
	  ellipse,
	  RUnit
Collate: AllGenerics.R
	 AllClasses.R
	 methods-AssayData.R
	 methods-CNSet.R
	 methods-CNSetLM.R
	 methods-eSet.R
         methods-SnpSuperSet.R
	 methods-PredictionRegion.R
         cnrma-functions.R
	 cnset-accessors.R
         crlmm-functions.R
	 crlmmGT2.R
         crlmm-illumina.R
	 snprma-functions.R
         utils.R
         zzz.R
	 test_crlmm_package.R
LazyLoad: yes
biocViews: Microarray, Preprocessing, SNP, Bioinformatics, CopyNumberVariants