Adding scater, ExpressionAtlas, RImmPort, chromPlot

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/scater@113892 bc3139a8-67e5-0310-9ffc-ced21a209358

DESCRIPTION

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+Package: scater
+Type: Package
+Maintainer: Davis McCarthy <[email protected]>
+Author: Davis McCarthy
+Authors@R: c(person("Davis", "McCarthy", role=c("aut", "cre"),
+        email="[email protected]"), person("Quin", "Wills",
+        role=c("aut"), email="[email protected]"), person("Kieran",
+        "Campbell", role=c("aut"),
+        email="[email protected]"))
+Version: 0.99.2
+Date: 2016-01-22
+License: GPL (>= 2)
+Title: Single-cell analysis toolkit for gene expression data in R
+Description: A collection of tools for doing various analyses of
+        single-cell RNA-seq gene expression data, with a focus on
+        quality control.
+Depends: R (>= 3.3), Biobase, ggplot2, methods
+Imports: biomaRt, data.table, dplyr, edgeR, grid, limma, matrixStats,
+        parallel, plyr, reshape2, rhdf5, rjson, viridis
+Suggests: BiocStyle, cowplot, cluster, destiny, knitr, monocle,
+        mvoutlier, rmarkdown, Rtsne, testthat
+VignetteBuilder: knitr
+LazyData: true
+biocViews: RNASeq, QualityControl, Preprocessing, Normalization,
+        Visualization, DimensionReduction, Transcriptomics,
+        GeneExpression, Sequencing, Software, DataImport,
+        DataRepresentation, Infrastructure
+RoxygenNote: 5.0.1
+NeedsCompilation: no

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export("bootstraps<-")
+export("cellDist<-")
+export("cellPairwiseDistances<-")
+export("counts<-")
+export("cpm<-")
+export("fData<-")
+export("featDist<-")
+export("featurePairwiseDistances<-")
+export("fpkm<-")
+export("is_exprs<-")
+export("norm_counts<-")
+export("norm_cpm<-")
+export("norm_exprs<-")
+export("norm_fpkm<-")
+export("norm_tpm<-")
+export("pData<-")
+export("redDim<-")
+export("reducedDimension<-")
+export("set_exprs<-")
+export("stand_exprs<-")
+export("tpm<-")
+export(bootstraps)
+export(bootstraps.SCESet)
+export(calcIsExprs)
+export(calculateFPKM)
+export(calculateQCMetrics)
+export(calculateTPM)
+export(cellDist)
+export(cellDistSCESet)
+export(cellNames)
+export(cellPairwiseDistances)
+export(cellPairwiseDistances.SCESet)
+export(counts)
+export(counts.SCESet)
+export(cpm)
+export(cpm.SCESet)
+export(featDist)
+export(featDistSCESet)
+export(featurePairwiseDistances)
+export(featurePairwiseDistancesSCESet)
+export(findImportantPCs)
+export(fpkm)
+export(fpkm.SCESet)
+export(fromCellDataSet)
+export(getBMFeatureAnnos)
+export(getExprs)
+export(get_exprs)
+export(get_exprs.SCESet)
+export(is_exprs)
+export(is_exprs.SCESet)
+export(multiplot)
+export(newSCESet)
+export(norm_counts)
+export(norm_counts.SCESet)
+export(norm_cpm)
+export(norm_cpm.SCESet)
+export(norm_exprs)
+export(norm_exprs.SCESet)
+export(norm_fpkm)
+export(norm_fpkm.SCESet)
+export(norm_tpm)
+export(norm_tpm.SCESet)
+export(normaliseExprs)
+export(normalizeExprs)
+export(plotDiffusionMap)
+export(plotDiffusionMapSCESet)
+export(plotExplanatoryVariables)
+export(plotExpression)
+export(plotExpressionDefault)
+export(plotExpressionSCESet)
+export(plotExprsFreqVsMean)
+export(plotFeatureData)
+export(plotHighestExprs)
+export(plotMetadata)
+export(plotPCA)
+export(plotPCASCESet)
+export(plotPhenoData)
+export(plotQC)
+export(plotReducedDim)
+export(plotReducedDim.SCESet)
+export(plotReducedDim.default)
+export(plotSCESet)
+export(plotTSNE)
+export(readKallistoResults)
+export(readKallistoResultsOneSample)
+export(readSalmonResults)
+export(readSalmonResultsOneSample)
+export(redDim)
+export(redDim.SCESet)
+export(reducedDimension)
+export(reducedDimension.SCESet)
+export(runKallisto)
+export(stand_exprs)
+export(stand_exprs.SCESet)
+export(summariseExprsAcrossFeatures)
+export(toCellDataSet)
+export(tpm)
+export(tpm.SCESet)
+exportClasses(SCESet)
+exportMethods("[")
+exportMethods("cellDist<-")
+exportMethods("cellPairwiseDistances<-")
+exportMethods("counts<-")
+exportMethods("cpm<-")
+exportMethods("fData<-")
+exportMethods("fpkm<-")
+exportMethods("is_exprs<-")
+exportMethods("norm_counts<-")
+exportMethods("norm_cpm<-")
+exportMethods("norm_exprs<-")
+exportMethods("norm_fpkm<-")
+exportMethods("norm_tpm<-")
+exportMethods("pData<-")
+exportMethods("redDim<-")
+exportMethods("reducedDimension<-")
+exportMethods("set_exprs<-")
+exportMethods("stand_exprs<-")
+exportMethods("tpm<-")
+exportMethods(bootstraps)
+exportMethods(cellDist)
+exportMethods(cellPairwiseDistances)
+exportMethods(counts)
+exportMethods(cpm)
+exportMethods(featDist)
+exportMethods(featurePairwiseDistances)
+exportMethods(fpkm)
+exportMethods(get_exprs)
+exportMethods(is_exprs)
+exportMethods(norm_counts)
+exportMethods(norm_cpm)
+exportMethods(norm_exprs)
+exportMethods(norm_fpkm)
+exportMethods(norm_tpm)
+exportMethods(plot)
+exportMethods(plotDiffusionMap)
+exportMethods(plotExpression)
+exportMethods(plotPCA)
+exportMethods(plotReducedDim)
+exportMethods(plotTSNE)
+exportMethods(redDim)
+exportMethods(reducedDimension)
+exportMethods(stand_exprs)
+exportMethods(tpm)
+import(ggplot2)
+import(methods)
+import(viridis)
+importFrom(Biobase,"fData<-")
+importFrom(Biobase,"pData<-")
+importFrom(Biobase,"sampleNames<-")
+importFrom(Biobase,"varMetadata<-")
+importFrom(Biobase,annotatedDataFrameFrom)
+importFrom(Biobase,assayDataNew)
+importFrom(Biobase,exprs)
+importFrom(Biobase,fData)
+importFrom(Biobase,featureData)
+importFrom(Biobase,featureNames)
+importFrom(Biobase,pData)
+importFrom(Biobase,phenoData)
+importFrom(Biobase,sampleNames)
+importFrom(Biobase,varLabels)
+importFrom(biomaRt,useMart)
+importFrom(data.table,fread)
+importFrom(dplyr,mutate)
+importFrom(edgeR,calcNormFactors.default)
+importFrom(edgeR,cpm.default)
+importFrom(grid,grid.layout)
+importFrom(grid,grid.newpage)
+importFrom(grid,pushViewport)
+importFrom(grid,viewport)
+importFrom(limma,lmFit)
+importFrom(matrixStats,colCumsums)
+importFrom(matrixStats,colVars)
+importFrom(matrixStats,rowVars)
+importFrom(parallel,makeCluster)
+importFrom(parallel,parLapply)
+importFrom(parallel,stopCluster)
+importFrom(plyr,aaply)
+importFrom(reshape2,melt)
+importFrom(rhdf5,H5close)
+importFrom(rhdf5,h5read)
+importFrom(rjson,fromJSON)

R/AllClasses.R

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+### all classes defined for the scater package
+
+################################################################################
+### defining the SCESet class
+
+#' The "Single Cell Expression Set" (SCESet)  class
+#'
+#' S4 class and the main class used by scater to hold single cell expression 
+#' data. SCESet extends the basic Bioconductor ExpressionSet class.
+#'
+#' This class is initialized from a matrix of expression values.
+#' 
+#' Methods that operate on SCESet objects constitute the basic scater workflow.
+#'
+#' Thanks to the Monocle package (github.com/cole-trapnell-lab/monocle-release/)
+#' for their CellDataSet class, which provided the inspiration and template for 
+#' SCESet.
+#'
+#'@section Slots:
+#'  \describe{
+#'    \item{\code{logged}:}{Scalar of class \code{"logical"}, indicating whether 
+#'    or not the expression data in the `exprs` slot have been log2-transformed
+#'    or not.}
+#'    \item{\code{logExprsOffset}:}{Scalar of class \code{"numeric"}, providing an offset 
+#'    applied to expression data in the `exprs` slot when undergoing log2-transformation
+#'    to avoid trying to take logs of zero.}
+#'    \item{\code{lowerDetectionLimit}:}{Scalar of class \code{"numeric"}, 
+#'    giving the lower limit for an expression value to be classified as 
+#'    "expressed".}
+#'    \item{\code{cellPairwiseDistances}:}{Matrix of class \code{"numeric"}, 
+#'    containing pairwise distances between cells.}
+#'    \item{\code{featurePairwiseDistances}:}{Matrix of class \code{"numeric"}, 
+#'    containing pairwise distances between features.}
+#'    \item{\code{reducedDimension}:}{Matrix of class \code{"numeric"}, containing
+#'    reduced-dimension coordinates for cells (generated, for example, by PCA).}
+#'    \item{\code{bootstraps}:}{Array of class \code{"numeric"} that can contain
+#'    bootstrap estimates of the expression or count values.}
+#'    \item{\code{useForExprs}:}{Character string (one of 'exprs','tpm','counts' or 'fpkm') indicating 
+#'    which expression representation both internal methods and external packages should use. 
+#'    Defaults to 'exprs'.}
+#'}
+#' @name SCESet
+#' @rdname SCESet
+#' @inheritParams Biobase ExpressionSet
+#' @aliases SCESet-class
+#' @exportClass SCESet
+setClass("SCESet",
+         contains = "ExpressionSet",
+         slots = c(logged = "logical",
+                   logExprsOffset = "numeric",
+                   lowerDetectionLimit = "numeric",
+                   cellPairwiseDistances = "matrix",
+                   featurePairwiseDistances = "matrix",
+                   reducedDimension = "matrix",
+                   bootstraps = "array",
+                   useForExprs = "character"),
+         prototype = prototype(new("VersionedBiobase",
+                                   versions = c(classVersion("ExpressionSet"),
+                                                SCESet = "0.1.6")))
+)
+
+