Browse code

Updated contact info and TODO

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@44787 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 22/02/2010 13:25:02
Showing 4 changed files

  • DESCRIPTION index feb7aa6..bc9c36b 100644
  • NAMESPACE index da834b4..ac2664e 100644
  • NEWS index ba63fad..fa7acf1 100644
  • TODO index 5a46dd0..f0a702d 100644
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@@ -1,16 +1,32 @@
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 Package: crlmm
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 Type: Package
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
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-Version: 1.5.26
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+Version: 1.5.27
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 Date: 2010-02-21
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-Author: Rafael A Irizarry, Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>
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-Maintainer: Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
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+Author: Rafael A Irizarry, Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>
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+Maintainer: Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
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 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
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 License: Artistic-2.0
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-Depends: R (>= 2.11.0), methods, Biobase (>= 2.7.2), oligoClasses (>= 1.9.28)
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-Imports: affyio (>= 1.15.2), preprocessCore, utils, stats, genefilter, splines, mvtnorm, ellipse, SNPchip
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+Depends: R (>= 2.11.0),
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+         methods,
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+         Biobase (>= 2.7.2),
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+         oligoClasses (>= 1.9.28)
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+Imports: affyio (>= 1.15.2),
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+         preprocessCore,
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+         utils,
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+         stats,
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+         genefilter,
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+         splines,
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+         mvtnorm,
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+         ellipse,
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+         SNPchip
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 Enhances: ff
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-Suggests: hapmapsnp5, hapmapsnp6, genomewidesnp5Crlmm (>= 1.0.2),genomewidesnp6Crlmm (>= 1.0.2), snpMatrix, metaArray
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+Suggests: hapmapsnp5,
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+          hapmapsnp6,
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+          genomewidesnp5Crlmm (>= 1.0.2),
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+          genomewidesnp6Crlmm (>= 1.0.2),
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+          snpMatrix,
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+          metaArray
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 Collate: AllClasses.R
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 	 AllGenerics.R
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 	 methods-CNSet.R
... ...
@@ -23,36 +23,51 @@ importFrom(Biobase, assayDataElement, assayDataElementNames,
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 importClassesFrom(oligoClasses, SnpSuperSet, AlleleSet)
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 importMethodsFrom(oligoClasses, allele, calls, "calls<-", confs,
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-		  "confs<-", cnConfidence, "cnConfidence<-", 
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-		  isSnp, chromosome, position, CA, "CA<-", CB, "CB<-", A, B)
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+		  "confs<-", cnConfidence, "cnConfidence<-", isSnp,
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+		  chromosome, position, CA, "CA<-", CB, "CB<-", A, B)
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+importFrom(oligoClasses, chromosome2integer, celfileDate, list.celfiles,
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+           copyNumber)
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-importFrom(oligoClasses, chromosome2integer, celfileDate, list.celfiles)
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-
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-importFrom(oligoClasses, copyNumber)
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-
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+## graphics
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 importFrom(graphics, abline, axis, layout, legend, mtext, par, plot,
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            polygon, rect, segments, text, points, boxplot)
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+## grDevices
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 importFrom(grDevices, grey)
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+## affyio
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 importFrom(affyio, read.celfile.header, read.celfile)
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-importFrom(preprocessCore, normalize.quantiles.use.target, normalize.quantiles)
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+## preprocessCore
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+importFrom(preprocessCore, normalize.quantiles.use.target,
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+           normalize.quantiles)
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-importFrom(utils, data, packageDescription, setTxtProgressBar, txtProgressBar)
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+## utils
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+importFrom(utils, data, packageDescription, setTxtProgressBar,
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+           txtProgressBar)
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-importFrom(stats, coef, cov, dnorm, kmeans, lm, mad, median, quantile, sd, update)
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+## stats
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+importFrom(stats, coef, cov, dnorm, kmeans, lm, mad, median, quantile,
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+           sd, update)
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+## genefilter
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 importFrom(genefilter, rowSds)
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+## mvtnorm
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 importFrom(mvtnorm, dmvnorm)
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+## ellipse
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 importFrom(ellipse, ellipse)
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 exportMethods(copyNumber)
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 export(cnOptions, crlmm, crlmmIllumina, crlmmCopynumber, ellipse, readIdatFiles, snprma, getParam) 
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+
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+#############
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+## TO REMOVE
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+#############
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+
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 ##export everything that does not start with a .
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 ##exportPattern("^[^\\.]")
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@@ -1,3 +1,17 @@
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+        **************************************************
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+        *                                                *
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+        *              1.5 SERIES NEWS                   *
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+        *                                                *
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+        **************************************************
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+
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+USER VISIBLE CHANGES
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+
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+NEW FEATURES
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+
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+	o Support to large datasets via ff package. The user
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+	must load the ff package manually to benefit from
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+	this.
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+
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         **************************************************
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         *                                                *
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         *              1.3 SERIES NEWS                   *
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@@ -21,7 +21,8 @@ R. Scharpf (after next release)
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 B Carvalho
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-- crlmm should return results in CHP files
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+- crlmm should return results in CHP files (still can't write CHP files)
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+- add parallel support (normalization and summarization)
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   ***********************************************************
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   *                                                         *