@@ -14,13 +14,15 @@ Description: Coordinated Gene Activity in Pattern Sets (CoGAPS)

 Maintainer: Elana J. Fertig <ejfertig@jhmi.edu>,

     Thomas D. Sherman <tomsherman159@gmail.com>

 Depends:

-    R (>= 3.4.0),

-    Rcpp (>= 0.11.0)

+    R (>= 3.5.0),

+    Rcpp

 Imports:

+    cluster,

     methods,

     gplots,

     graphics,

-    S4Vectors

+    S4Vectors,

+    SingleCellExperiment

 Suggests:

     testthat,

     knitr,

@@ -33,7 +35,7 @@ biocViews: GeneExpression, Transcription, GeneSetEnrichment,

     DifferentialExpression, Bayesian, Clustering, TimeCourse, RNASeq, Microarray,

     MultipleComparison, DimensionReduction

 NeedsCompilation: yes

-RoxygenNote: 5.0.1

+RoxygenNote: 6.0.1

 Collate:

     'class-CogapsParams.R'

     'CoGAPS.R'

@@ -1,5 +1,6 @@

 # Generated by roxygen2: do not edit by hand

+S3method(plot,CogapsResult)

 export(CoGAPS)

 export(binaryA)

 export(buildReport)

@@ -11,18 +12,20 @@ export(getMeanChiSq)

 export(getParam)

 export(patternMarkers)

 export(patternMatch)

-export(plot.CogapsResult)

 export(plotPatternMarkers)

 export(plotResiduals)

 export(reconstructGene)

 export(setParam)

 exportClasses(CogapsParams)

 exportClasses(CogapsResult)

-importClassesFrom(S4Vectors,Annotated)

-importClassesFrom(S4Vectors,DataFrame)

-importClassesFrom(S4Vectors,character_OR_NULL)

+importClassesFrom(SingleCellExperiment,LinearEmbeddingMatrix)

+importFrom(cluster,agnes)

 importFrom(gplots,bluered)

+importFrom(gplots,heatmap.2)

 importFrom(graphics,plot)

 importFrom(methods,callNextMethod)

 importFrom(methods,new)

+importFrom(stats,as.hclust)

+importFrom(stats,cutree)

+importFrom(stats,hclust)

 useDynLib(CoGAPS)

@@ -137,6 +137,12 @@ checkpointInFile=NULL, transposeData=FALSE, ...)

         ...)

 }   

+parseExtraParams <- function(allParams, extraParams)

+{

+

+

+}

+

 #' Check that provided data is valid

 #'

 #' @param data data matrix

@@ -1,7 +1,25 @@

 #' CogapsParams

 #' @export 

+#' @rdname CogapsParams-class

 #'

 #' @description Encapsulates all parameters for the CoGAPS algorithm

+#' @slot nPatterns number of patterns CoGAPS will learn

+#' @slot nIterations number of iterations for each phase of the algorithm

+#' @slot alphaA sparsity parameter for feature matrix

+#' @slot alphaP sparsity parameter for sample matrix

+#' @slot maxGibbsMassA atomic mass restriction for feature matrix

+#' @slot maxGibbsMassP atomic mass restriction for sample matrix

+#' @slot seed random number generator seed

+#' @slot singleCell is the data single cell?

+#' @slot distributed either "genome-wide" or "single-cell" indicating which

+#' distributed algorithm should be used

+#' @slot nSets [distributed parameter] number of sets to break data into

+#' @slot cut [distributed parameter] number of branches at which to cut

+#' dendrogram used in pattern matching

+#' @slot minNS [distributed parameter] minimum of individual set contributions

+#' a cluster must contain

+#' @slot maxNS [distributed parameter] maximum of individual set contributions

+#' a cluster can contain

 setClass("CogapsParams", slots = c(

     nPatterns = "numeric",

     nIterations = "numeric",

@@ -12,8 +30,8 @@ setClass("CogapsParams", slots = c(

     seed = "numeric",

     singleCell = "logical",

     distributed = "character",

-    nSets = "numeric",

     cut = "numeric",

+    nSets = "numeric",

     minNS = "numeric",

     maxNS = "numeric"

 ))

@@ -35,8 +53,8 @@ setMethod("initialize", "CogapsParams",

         .Object@seed <- getMilliseconds(as.POSIXlt(Sys.time()))

         .Object@singleCell <- FALSE

         .Object@distributed <- ""

-        .Object@nSets <- 3

         .Object@cut <- .Object@nPatterns

+        .Object@nSets <- 3

         .Object@minNS <- ceiling(.Object@nSets / 2)

         .Object@maxNS <- .Object@minNS + .Object@nSets

@@ -2,10 +2,10 @@

 #' @export

 #'

 #' @description Contains all output from Cogaps run

-#' @importClassesFrom S4Vectors DataFrame Annotated character_OR_NULL

+#' @importClassesFrom SingleCellExperiment LinearEmbeddingMatrix

 setClass("CogapsResult", contains="LinearEmbeddingMatrix", slots=c(

     sampleStdDev = "ANY",   # Psd transpose

-    featureStdDev = "ANY",  # Asd

+    featureStdDev = "ANY"   # Asd

 ))

 #' Constructor for CogapsResult

@@ -1,3 +1,18 @@

+setMethod("show", signature("CogapsParams"),

+function(object)

+{

+    cat("An Object of class \"CogapsParams\"\n")

+    cat("nPatterns          ", object@nPatterns, "\n")

+    cat("nIterations        ", object@nIterations, "\n")

+    cat("outputFrequency    ", object@outputFrequency, "\n")

+    cat("nCores             ", object@nCores, "\n")

+    cat("singleCell         ", object@singleCell, "\n")

+    cat("seed               ", object@seed, "\n")

+    cat("messages           ", object@messages, "\n")

+    cat("checkpointInterval ", object@checkpointInterval, "\n")

+    cat("checkpointOutFile  ", object@checkpointOutFile, "\n")

+})

+

 #' @rdname setParam-methods

 #' @aliases setParam

 setMethod("setParam", signature(object="CogapsParams"),

@@ -74,20 +89,4 @@ function(object, args)

         }

     }

     return(object)

-})

-

-setMethod("show", signature("CogapsParams"),

-function(object)

-{

-    cat("An Object of class \"CogapsParams\"\n")

-    cat("nPatterns          ", object@nPatterns, "\n")

-    cat("nIterations        ", object@nIterations, "\n")

-    cat("outputFrequency    ", object@outputFrequency, "\n")

-    cat("nCores             ", object@nCores, "\n")

-    cat("singleCell         ", object@singleCell, "\n")

-    cat("seed               ", object@seed, "\n")

-    cat("messages           ", object@messages, "\n")

-    cat("checkpointInterval ", object@checkpointInterval, "\n")

-    cat("checkpointOutFile  ", object@checkpointOutFile, "\n")

-})

-

+})

\ No newline at end of file

@@ -225,7 +225,7 @@ samplePalette=NULL, heatmapCol=bluered, colDenogram=TRUE, scale="row", ...)

         ColSideColors=as.character(samplePalette),

         rowsep=cumsum(sapply(patternMarkers,length))

     )

-})

+}

 #' @rdname calcCoGAPSStat-methods

 #' @aliases calcCoGAPSStat

@@ -49,4 +49,3 @@ params <- new("CogapsParams")

 params <- setParam(params, "nPatterns", 5)

 resultC <- CoGAPS(GIST.D, params)

 }

-

@@ -18,14 +18,13 @@ Date: \tab 2018-01-24\cr

 License: \tab LGPL\cr

 }

 }

-\author{

-Maintainer: Elana J. Fertig \email{ejfertig@jhmi.edu},

-            Michael F. Ochs \email{ochsm@tcnj.edu}

-}

 \references{

 Fertig EJ, Ding J, Favorov AV, Parmigiani G, Ochs MF.

 CoGAPS: an R/C++ package to identify patterns and biological

 process activity in transcriptomic data.

 Bioinformatics. 2010 Nov 1;26(21):2792-3

 }

-

+\author{

+Maintainer: Elana J. Fertig \email{ejfertig@jhmi.edu},

+            Michael F. Ochs \email{ochsm@tcnj.edu}

+}

@@ -7,4 +7,37 @@

 \description{

 Encapsulates all parameters for the CoGAPS algorithm

 }

+\section{Slots}{

+

+\describe{

+\item{\code{nPatterns}}{number of patterns CoGAPS will learn}

+

+\item{\code{nIterations}}{number of iterations for each phase of the algorithm}

+

+\item{\code{alphaA}}{sparsity parameter for feature matrix}

+

+\item{\code{alphaP}}{sparsity parameter for sample matrix}

+

+\item{\code{maxGibbsMassA}}{atomic mass restriction for feature matrix}

+

+\item{\code{maxGibbsMassP}}{atomic mass restriction for sample matrix}

+

+\item{\code{seed}}{random number generator seed}

+

+\item{\code{singleCell}}{is the data single cell?}

+

+\item{\code{distributed}}{either "genome-wide" or "single-cell" indicating which

+distributed algorithm should be used}

+

+\item{\code{nSets}}{[distributed parameter] number of sets to break data into}

+

+\item{\code{cut}}{[distributed parameter] number of branches at which to cut

+dendrogram used in pattern matching}

+

+\item{\code{minNS}}{[distributed parameter] minimum of individual set contributions

+a cluster must contain}

+

+\item{\code{maxNS}}{[distributed parameter] maximum of individual set contributions

+a cluster can contain}

+}}

@@ -7,4 +7,3 @@

 \description{

 Contains all output from Cogaps run

 }

-

@@ -10,4 +10,3 @@ GIST.D

 \description{

 Sample GIST gene expression data from Ochs et al. (2009)

 }

-

@@ -10,4 +10,3 @@ GIST.GeneSets

 \description{

 Simulated dataset to quantify gene set membership in the GIST dataset

 }

-

@@ -10,4 +10,3 @@ GIST.S

 \description{

 Sample GIST gene expression data from Ochs et al. (2009)

 }

-

@@ -10,4 +10,3 @@ GIST.result

 \description{

 CoGAPS result from running on GIST dataset

 }

-

@@ -10,4 +10,3 @@ GSets

 \description{

 Simulated dataset to quantify gene set membership.

 }

-

@@ -10,4 +10,3 @@ SimpSim.A

 \description{

 Simulated data

 }

-

@@ -10,4 +10,3 @@ SimpSim.D

 \description{

 Simulated data

 }

-

@@ -10,4 +10,3 @@ SimpSim.P

 \description{

 Simulated data

 }

-

@@ -10,4 +10,3 @@ SimpSim.S

 \description{

 Simulated data

 }

-

@@ -10,4 +10,3 @@ SimpSim.result

 \description{

 CoGAPS result from running on simulated data

 }

-

@@ -1,9 +1,10 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/class-CogapsResult.R

+% Please edit documentation in R/class-CogapsResult.R, R/methods-CogapsResult.R

 \docType{methods}

 \name{binaryA}

 \alias{binaryA}

 \alias{binaryA,CogapsResult-method}

+\alias{binaryA}

 \title{binary heatmap for standardized feature matrix}

 \usage{

 binaryA(object, threshold = 3)

@@ -29,4 +30,3 @@ data(SimpSim)

 result <- CoGAPS(SimpSim.D)

 binMatrix <- binaryA(result, threshold=3)

 }

-

@@ -19,4 +19,3 @@ returns information about how the package was compiled, i.e. which

 \examples{

 CoGAPS::buildReport()

 }

-

@@ -1,9 +1,10 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/class-CogapsResult.R

+% Please edit documentation in R/class-CogapsResult.R, R/methods-CogapsResult.R

 \docType{methods}

 \name{calcCoGAPSStat}

 \alias{calcCoGAPSStat}

 \alias{calcCoGAPSStat,CogapsResult-method}

+\alias{calcCoGAPSStat}

 \title{calculate gene set statistics}

 \usage{

 calcCoGAPSStat(object, GStoGenes, numPerm = 500)

@@ -30,4 +31,3 @@ data('SimpSim')

 result <- CoGAPS(SimpSim.D)

 calcCoGAPSStat(result, GStoGenes=GSets, numPerm=500)

 }

-

@@ -1,9 +1,10 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/class-CogapsResult.R

+% Please edit documentation in R/class-CogapsResult.R, R/methods-CogapsResult.R

 \docType{methods}

 \name{calcGeneGSStat}

 \alias{calcGeneGSStat}

 \alias{calcGeneGSStat,CogapsResult-method}

+\alias{calcGeneGSStat}

 \title{probability gene belongs in gene set}

 \usage{

 calcGeneGSStat(object, GStoGenes, numPerm, Pw = rep(1, ncol(Amean)),

@@ -36,4 +37,3 @@ data(SimpSim)

 result <- CoGAPS(SimpSim.D)

 calcGeneGSStat(result, GSGenes=GSets[[1]], numPerm=500)

 }

-

@@ -1,9 +1,10 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/class-CogapsResult.R

+% Please edit documentation in R/class-CogapsResult.R, R/methods-CogapsResult.R

 \docType{methods}

 \name{calcZ}

 \alias{calcZ}

 \alias{calcZ,CogapsResult-method}

+\alias{calcZ}

 \title{compute z-score matrix}

 \usage{

 calcZ(object, which = "feature")

@@ -28,4 +29,3 @@ data(SimpSim)

 result <- CoGAPS(SimpSim.D)

 feature_zscore <- calcZ(result)

 }

-

@@ -17,4 +17,3 @@ throws an error if data has problems

 \description{

 Check that provided data is valid

 }

-

@@ -1,9 +1,10 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/class-CogapsResult.R

+% Please edit documentation in R/class-CogapsResult.R, R/methods-CogapsResult.R

 \docType{methods}

 \name{computeGeneGSProb}

 \alias{computeGeneGSProb}

 \alias{computeGeneGSProb,CogapsResult-method}

+\alias{computeGeneGSProb}

 \title{compute gene probability}

 \usage{

 computeGeneGSProb(object, GStoGenes, numPerm = 500, Pw = rep(1,

@@ -39,4 +40,3 @@ data(SimpSim)

 result <- CoGAPS(SimpSim.D)

 computeGeneGSProb(result, GSGenes=GSets[[1]], numPerm=500)

 }

-

@@ -23,4 +23,3 @@ back together

 \details{

 For file types CoGAPS supports csv, tsv, and mtx

 }

-

@@ -1,9 +1,10 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/class-CogapsResult.R

+% Please edit documentation in R/class-CogapsResult.R, R/methods-CogapsResult.R

 \docType{methods}

 \name{getMeanChiSq}

 \alias{getMeanChiSq}

 \alias{getMeanChiSq,CogapsResult-method}

+\alias{getMeanChiSq}

 \title{return chi-sq of final matrices}

 \usage{

 getMeanChiSq(object)

@@ -22,4 +23,3 @@ meanChiSq(result)

 \description{

 return chi-sq of final matrices

 }

-

@@ -1,9 +1,10 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/class-CogapsParams.R

+% Please edit documentation in R/class-CogapsParams.R, R/methods-CogapsParams.R

 \docType{methods}

 \name{getParam}

 \alias{getParam}

 \alias{getParam,CogapsParams-method}

+\alias{getParam}

 \title{get the value of a parameter}

 \usage{

 getParam(object, whichParam)

@@ -25,4 +26,3 @@ get the value of a parameter

  params <- new("CogapsParams")

  getParam(params, "seed")

 }

-

@@ -13,4 +13,3 @@ initialized CogapsParams object

 \description{

 Constructor for CogapsParams

 }

-

@@ -14,4 +14,3 @@ initialized CogapsResult object

 \description{

 Constructor for CogapsResult

 }

-

@@ -1,9 +1,10 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/class-CogapsParams.R

+% Please edit documentation in R/class-CogapsParams.R, R/methods-CogapsParams.R

 \docType{methods}

 \name{parseDirectParams}

 \alias{parseDirectParams}

 \alias{parseDirectParams,CogapsParams-method}

+\alias{parseDirectParams}

 \title{parse list of parameters passed directly to CoGAPS}

 \usage{

 parseDirectParams(object, args)

@@ -21,4 +22,3 @@ an object of type CogapsParams

 \description{

 parse list of parameters passed directly to CoGAPS

 }

-

@@ -1,9 +1,10 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/class-CogapsParams.R

+% Please edit documentation in R/class-CogapsParams.R, R/methods-CogapsParams.R

 \docType{methods}

 \name{parseOldParams}

 \alias{parseOldParams}

 \alias{parseOldParams,CogapsParams-method}

+\alias{parseOldParams}

 \title{parse list of old-style parameters, store relevant values}

 \usage{

 parseOldParams(object, oldArgs)

@@ -21,4 +22,3 @@ an object of type CogapsParams

 \description{

 parse list of old-style parameters, store relevant values

 }

-

@@ -1,15 +1,15 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/class-CogapsResult.R

+% Please edit documentation in R/class-CogapsResult.R, R/methods-CogapsResult.R

 \docType{methods}

 \name{patternMarkers}

 \alias{patternMarkers}

 \alias{patternMarkers,CogapsResult-method}

+\alias{patternMarkers}

 \title{compute pattern markers statistic}

 \usage{

 patternMarkers(object, threshold = "all", lp = NA, full = FALSE)

-\S4method{patternMarkers}{CogapsResult}(object, threshold = "all", lp = NA,

-  full = FALSE)

+\S4method{patternMarkers}{CogapsResult}(object, threshold, lp)

 }

 \arguments{

 \item{object}{an object of type CogapsResult}

@@ -20,9 +20,6 @@ by the first gene to have a lower ranking, i.e. better fit to, a pattern.}

 \item{lp}{a vector of weights for each pattern to be used for finding

 markers. If NA markers for each pattern of the A matrix will be used.}

-

-\item{full}{logical indicating whether to return the ranks of each gene for

-each pattern}

 }

 \value{

 By default a non-overlapping list of genes associated with each

@@ -32,4 +29,3 @@ for each \code{lp} will also be returned.

 \description{

 calculate the most associated pattern for each gene

 }

-

@@ -30,4 +30,3 @@ consensus pattern is also returned.

 \description{

 Match Patterns Across Multiple Runs

 }

-

@@ -1,18 +1,13 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/class-CogapsResult.R

+% Please edit documentation in R/methods-CogapsResult.R

 \docType{methods}

 \name{plotPatternMarkers}

 \alias{plotPatternMarkers}

-\alias{plotPatternMarkers,CogapsResult-method}

 \title{heatmap of original data clustered by pattern markers statistic}

 \usage{

 plotPatternMarkers(object, data, patternPalette, sampleNames,

   samplePalette = NULL, heatmapCol = bluered, colDenogram = TRUE,

   scale = "row", ...)

-

-\S4method{plotPatternMarkers}{CogapsResult}(object, data, patternPalette,

-  sampleNames, samplePalette = NULL, heatmapCol = bluered,

-  colDenogram = TRUE, scale = "row", ...)

 }

 \arguments{

 \item{object}{an object of type CogapsResult}

@@ -46,4 +41,3 @@ heatmap of original data clustered by pattern markers statistic

 \seealso{

 \code{\link{heatmap.2}}

 }

-

@@ -1,9 +1,10 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/class-CogapsResult.R

+% Please edit documentation in R/class-CogapsResult.R, R/methods-CogapsResult.R

 \docType{methods}

 \name{plotResiduals}

 \alias{plotResiduals}

 \alias{plotResiduals,CogapsResult-method}

+\alias{plotResiduals}

 \title{plot of residuals}

 \usage{

 plotResiduals(object, data, uncertainty = NULL)

@@ -28,4 +29,3 @@ data(SimpSim)

 result <- CoGAPS(SimpSim.D)

 plotResiduals(result, SimpSim.D)

 }

-

@@ -1,9 +1,10 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/class-CogapsResult.R

+% Please edit documentation in R/class-CogapsResult.R, R/methods-CogapsResult.R

 \docType{methods}

 \name{reconstructGene}

 \alias{reconstructGene}

 \alias{reconstructGene,CogapsResult-method}

+\alias{reconstructGene}

 \title{reconstruct gene}

 \usage{

 reconstructGene(object, genes = NULL)

@@ -26,4 +27,3 @@ data(SimpSim)

 result <- CoGAPS(SimpSim.D)

 D_estimate <- reconstructGene(result)

 }

-

@@ -1,9 +1,10 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/class-CogapsParams.R

+% Please edit documentation in R/class-CogapsParams.R, R/methods-CogapsParams.R

 \docType{methods}

 \name{setParam}

 \alias{setParam}

 \alias{setParam,CogapsParams-method}

+\alias{setParam}

 \title{set the value of a parameter}

 \usage{

 setParam(object, whichParam, value)

@@ -27,4 +28,3 @@ set the value of a parameter

  params <- new("CogapsParams")

  params <- setParam(params, "seed", 123)

 }

-

@@ -10,4 +10,3 @@ tf2ugFC

 \description{

 Gene sets defined by transcription factors defined from TRANSFAC.

 }

-