Tom Sherman authored on 26/07/2018 19:21:36
Showing42 changed files

... ...
@@ -14,13 +14,15 @@ Description: Coordinated Gene Activity in Pattern Sets (CoGAPS)
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 Maintainer: Elana J. Fertig <ejfertig@jhmi.edu>,
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     Thomas D. Sherman <tomsherman159@gmail.com>
16 16
 Depends:
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-    R (>= 3.4.0),
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-    Rcpp (>= 0.11.0)
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+    R (>= 3.5.0),
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+    Rcpp
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 Imports:
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+    cluster,
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     methods,
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     gplots,
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     graphics,
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-    S4Vectors
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+    S4Vectors,
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+    SingleCellExperiment
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 Suggests:
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     testthat,
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     knitr,
... ...
@@ -33,7 +35,7 @@ biocViews: GeneExpression, Transcription, GeneSetEnrichment,
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     DifferentialExpression, Bayesian, Clustering, TimeCourse, RNASeq, Microarray,
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     MultipleComparison, DimensionReduction
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 NeedsCompilation: yes
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-RoxygenNote: 5.0.1
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+RoxygenNote: 6.0.1
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 Collate:
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     'class-CogapsParams.R'
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     'CoGAPS.R'
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@@ -1,5 +1,6 @@
1 1
 # Generated by roxygen2: do not edit by hand
2 2
 
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+S3method(plot,CogapsResult)
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 export(CoGAPS)
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 export(binaryA)
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 export(buildReport)
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@@ -11,18 +12,20 @@ export(getMeanChiSq)
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 export(getParam)
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 export(patternMarkers)
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 export(patternMatch)
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-export(plot.CogapsResult)
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 export(plotPatternMarkers)
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 export(plotResiduals)
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 export(reconstructGene)
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 export(setParam)
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 exportClasses(CogapsParams)
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 exportClasses(CogapsResult)
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-importClassesFrom(S4Vectors,Annotated)
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-importClassesFrom(S4Vectors,DataFrame)
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-importClassesFrom(S4Vectors,character_OR_NULL)
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+importClassesFrom(SingleCellExperiment,LinearEmbeddingMatrix)
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+importFrom(cluster,agnes)
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 importFrom(gplots,bluered)
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+importFrom(gplots,heatmap.2)
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 importFrom(graphics,plot)
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 importFrom(methods,callNextMethod)
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 importFrom(methods,new)
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+importFrom(stats,as.hclust)
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+importFrom(stats,cutree)
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+importFrom(stats,hclust)
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 useDynLib(CoGAPS)
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@@ -137,6 +137,12 @@ checkpointInFile=NULL, transposeData=FALSE, ...)
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         ...)
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 }   
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+parseExtraParams <- function(allParams, extraParams)
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+{
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+
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+
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+}
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+
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 #' Check that provided data is valid
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 #'
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 #' @param data data matrix
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@@ -1,7 +1,25 @@
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 #' CogapsParams
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 #' @export 
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+#' @rdname CogapsParams-class
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 #'
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 #' @description Encapsulates all parameters for the CoGAPS algorithm
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+#' @slot nPatterns number of patterns CoGAPS will learn
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+#' @slot nIterations number of iterations for each phase of the algorithm
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+#' @slot alphaA sparsity parameter for feature matrix
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+#' @slot alphaP sparsity parameter for sample matrix
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+#' @slot maxGibbsMassA atomic mass restriction for feature matrix
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+#' @slot maxGibbsMassP atomic mass restriction for sample matrix
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+#' @slot seed random number generator seed
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+#' @slot singleCell is the data single cell?
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+#' @slot distributed either "genome-wide" or "single-cell" indicating which
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+#' distributed algorithm should be used
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+#' @slot nSets [distributed parameter] number of sets to break data into
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+#' @slot cut [distributed parameter] number of branches at which to cut
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+#' dendrogram used in pattern matching
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+#' @slot minNS [distributed parameter] minimum of individual set contributions
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+#' a cluster must contain
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+#' @slot maxNS [distributed parameter] maximum of individual set contributions
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+#' a cluster can contain
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 setClass("CogapsParams", slots = c(
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     nPatterns = "numeric",
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     nIterations = "numeric",
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@@ -12,8 +30,8 @@ setClass("CogapsParams", slots = c(
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     seed = "numeric",
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     singleCell = "logical",
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     distributed = "character",
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-    nSets = "numeric",
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     cut = "numeric",
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+    nSets = "numeric",
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     minNS = "numeric",
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     maxNS = "numeric"
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 ))
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@@ -35,8 +53,8 @@ setMethod("initialize", "CogapsParams",
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         .Object@seed <- getMilliseconds(as.POSIXlt(Sys.time()))
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         .Object@singleCell <- FALSE
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         .Object@distributed <- ""
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-        .Object@nSets <- 3
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         .Object@cut <- .Object@nPatterns
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+        .Object@nSets <- 3
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         .Object@minNS <- ceiling(.Object@nSets / 2)
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         .Object@maxNS <- .Object@minNS + .Object@nSets
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... ...
@@ -2,10 +2,10 @@
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 #' @export
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 #'
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 #' @description Contains all output from Cogaps run
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-#' @importClassesFrom S4Vectors DataFrame Annotated character_OR_NULL
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+#' @importClassesFrom SingleCellExperiment LinearEmbeddingMatrix
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 setClass("CogapsResult", contains="LinearEmbeddingMatrix", slots=c(
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     sampleStdDev = "ANY",   # Psd transpose
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-    featureStdDev = "ANY",  # Asd
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+    featureStdDev = "ANY"   # Asd
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 ))
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 #' Constructor for CogapsResult
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@@ -1,3 +1,18 @@
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+setMethod("show", signature("CogapsParams"),
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+function(object)
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+{
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+    cat("An Object of class \"CogapsParams\"\n")
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+    cat("nPatterns          ", object@nPatterns, "\n")
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+    cat("nIterations        ", object@nIterations, "\n")
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+    cat("outputFrequency    ", object@outputFrequency, "\n")
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+    cat("nCores             ", object@nCores, "\n")
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+    cat("singleCell         ", object@singleCell, "\n")
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+    cat("seed               ", object@seed, "\n")
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+    cat("messages           ", object@messages, "\n")
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+    cat("checkpointInterval ", object@checkpointInterval, "\n")
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+    cat("checkpointOutFile  ", object@checkpointOutFile, "\n")
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+})
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+
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 #' @rdname setParam-methods
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 #' @aliases setParam
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 setMethod("setParam", signature(object="CogapsParams"),
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@@ -74,20 +89,4 @@ function(object, args)
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         }
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     }
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     return(object)
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-})
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-
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-setMethod("show", signature("CogapsParams"),
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-function(object)
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-{
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-    cat("An Object of class \"CogapsParams\"\n")
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-    cat("nPatterns          ", object@nPatterns, "\n")
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-    cat("nIterations        ", object@nIterations, "\n")
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-    cat("outputFrequency    ", object@outputFrequency, "\n")
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-    cat("nCores             ", object@nCores, "\n")
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-    cat("singleCell         ", object@singleCell, "\n")
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-    cat("seed               ", object@seed, "\n")
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-    cat("messages           ", object@messages, "\n")
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-    cat("checkpointInterval ", object@checkpointInterval, "\n")
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-    cat("checkpointOutFile  ", object@checkpointOutFile, "\n")
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-})
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-
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+})
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\ No newline at end of file
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@@ -225,7 +225,7 @@ samplePalette=NULL, heatmapCol=bluered, colDenogram=TRUE, scale="row", ...)
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         ColSideColors=as.character(samplePalette),
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         rowsep=cumsum(sapply(patternMarkers,length))
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     )
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-})
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+}
229 229
 
230 230
 #' @rdname calcCoGAPSStat-methods
231 231
 #' @aliases calcCoGAPSStat
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@@ -49,4 +49,3 @@ params <- new("CogapsParams")
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 params <- setParam(params, "nPatterns", 5)
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 resultC <- CoGAPS(GIST.D, params)
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 }
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-
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@@ -18,14 +18,13 @@ Date: \tab 2018-01-24\cr
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 License: \tab LGPL\cr
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 }
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 }
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-\author{
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-Maintainer: Elana J. Fertig \email{ejfertig@jhmi.edu},
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-            Michael F. Ochs \email{ochsm@tcnj.edu}
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-}
25 21
 \references{
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 Fertig EJ, Ding J, Favorov AV, Parmigiani G, Ochs MF.
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 CoGAPS: an R/C++ package to identify patterns and biological
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 process activity in transcriptomic data.
29 25
 Bioinformatics. 2010 Nov 1;26(21):2792-3
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 }
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-
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+\author{
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+Maintainer: Elana J. Fertig \email{ejfertig@jhmi.edu},
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+            Michael F. Ochs \email{ochsm@tcnj.edu}
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+}
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@@ -7,4 +7,37 @@
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 \description{
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 Encapsulates all parameters for the CoGAPS algorithm
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 }
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+\section{Slots}{
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+
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+\describe{
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+\item{\code{nPatterns}}{number of patterns CoGAPS will learn}
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+
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+\item{\code{nIterations}}{number of iterations for each phase of the algorithm}
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+
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+\item{\code{alphaA}}{sparsity parameter for feature matrix}
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+
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+\item{\code{alphaP}}{sparsity parameter for sample matrix}
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+
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+\item{\code{maxGibbsMassA}}{atomic mass restriction for feature matrix}
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+
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+\item{\code{maxGibbsMassP}}{atomic mass restriction for sample matrix}
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+
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+\item{\code{seed}}{random number generator seed}
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+
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+\item{\code{singleCell}}{is the data single cell?}
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+
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+\item{\code{distributed}}{either "genome-wide" or "single-cell" indicating which
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+distributed algorithm should be used}
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+
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+\item{\code{nSets}}{[distributed parameter] number of sets to break data into}
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+
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+\item{\code{cut}}{[distributed parameter] number of branches at which to cut
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+dendrogram used in pattern matching}
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+
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+\item{\code{minNS}}{[distributed parameter] minimum of individual set contributions
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+a cluster must contain}
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+
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+\item{\code{maxNS}}{[distributed parameter] maximum of individual set contributions
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+a cluster can contain}
42
+}}
10 43
 
... ...
@@ -7,4 +7,3 @@
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 \description{
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 Contains all output from Cogaps run
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 }
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-
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@@ -10,4 +10,3 @@ GIST.D
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 \description{
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 Sample GIST gene expression data from Ochs et al. (2009)
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 }
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-
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@@ -10,4 +10,3 @@ GIST.GeneSets
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 \description{
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 Simulated dataset to quantify gene set membership in the GIST dataset
12 12
 }
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-
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@@ -10,4 +10,3 @@ GIST.S
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 \description{
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 Sample GIST gene expression data from Ochs et al. (2009)
12 12
 }
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-
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@@ -10,4 +10,3 @@ GIST.result
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 \description{
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 CoGAPS result from running on GIST dataset
12 12
 }
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-
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@@ -10,4 +10,3 @@ GSets
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 \description{
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 Simulated dataset to quantify gene set membership.
12 12
 }
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-
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@@ -10,4 +10,3 @@ SimpSim.A
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 \description{
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 Simulated data
12 12
 }
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-
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@@ -10,4 +10,3 @@ SimpSim.D
10 10
 \description{
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 Simulated data
12 12
 }
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-
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@@ -10,4 +10,3 @@ SimpSim.P
10 10
 \description{
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 Simulated data
12 12
 }
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-
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@@ -10,4 +10,3 @@ SimpSim.S
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 \description{
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 Simulated data
12 12
 }
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-
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@@ -10,4 +10,3 @@ SimpSim.result
10 10
 \description{
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 CoGAPS result from running on simulated data
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 }
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-
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@@ -1,9 +1,10 @@
1 1
 % Generated by roxygen2: do not edit by hand
2
-% Please edit documentation in R/class-CogapsResult.R
2
+% Please edit documentation in R/class-CogapsResult.R, R/methods-CogapsResult.R
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 \docType{methods}
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 \name{binaryA}
5 5
 \alias{binaryA}
6 6
 \alias{binaryA,CogapsResult-method}
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+\alias{binaryA}
7 8
 \title{binary heatmap for standardized feature matrix}
8 9
 \usage{
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 binaryA(object, threshold = 3)
... ...
@@ -29,4 +30,3 @@ data(SimpSim)
29 30
 result <- CoGAPS(SimpSim.D)
30 31
 binMatrix <- binaryA(result, threshold=3)
31 32
 }
32
-
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@@ -19,4 +19,3 @@ returns information about how the package was compiled, i.e. which
19 19
 \examples{
20 20
 CoGAPS::buildReport()
21 21
 }
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-
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@@ -1,9 +1,10 @@
1 1
 % Generated by roxygen2: do not edit by hand
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-% Please edit documentation in R/class-CogapsResult.R
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+% Please edit documentation in R/class-CogapsResult.R, R/methods-CogapsResult.R
3 3
 \docType{methods}
4 4
 \name{calcCoGAPSStat}
5 5
 \alias{calcCoGAPSStat}
6 6
 \alias{calcCoGAPSStat,CogapsResult-method}
7
+\alias{calcCoGAPSStat}
7 8
 \title{calculate gene set statistics}
8 9
 \usage{
9 10
 calcCoGAPSStat(object, GStoGenes, numPerm = 500)
... ...
@@ -30,4 +31,3 @@ data('SimpSim')
30 31
 result <- CoGAPS(SimpSim.D)
31 32
 calcCoGAPSStat(result, GStoGenes=GSets, numPerm=500)
32 33
 }
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-
... ...
@@ -1,9 +1,10 @@
1 1
 % Generated by roxygen2: do not edit by hand
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-% Please edit documentation in R/class-CogapsResult.R
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+% Please edit documentation in R/class-CogapsResult.R, R/methods-CogapsResult.R
3 3
 \docType{methods}
4 4
 \name{calcGeneGSStat}
5 5
 \alias{calcGeneGSStat}
6 6
 \alias{calcGeneGSStat,CogapsResult-method}
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+\alias{calcGeneGSStat}
7 8
 \title{probability gene belongs in gene set}
8 9
 \usage{
9 10
 calcGeneGSStat(object, GStoGenes, numPerm, Pw = rep(1, ncol(Amean)),
... ...
@@ -36,4 +37,3 @@ data(SimpSim)
36 37
 result <- CoGAPS(SimpSim.D)
37 38
 calcGeneGSStat(result, GSGenes=GSets[[1]], numPerm=500)
38 39
 }
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-
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@@ -1,9 +1,10 @@
1 1
 % Generated by roxygen2: do not edit by hand
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-% Please edit documentation in R/class-CogapsResult.R
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+% Please edit documentation in R/class-CogapsResult.R, R/methods-CogapsResult.R
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 \docType{methods}
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 \name{calcZ}
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 \alias{calcZ}
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 \alias{calcZ,CogapsResult-method}
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+\alias{calcZ}
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 \title{compute z-score matrix}
8 9
 \usage{
9 10
 calcZ(object, which = "feature")
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@@ -28,4 +29,3 @@ data(SimpSim)
28 29
 result <- CoGAPS(SimpSim.D)
29 30
 feature_zscore <- calcZ(result)
30 31
 }
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-
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@@ -17,4 +17,3 @@ throws an error if data has problems
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 \description{
18 18
 Check that provided data is valid
19 19
 }
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-
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@@ -1,9 +1,10 @@
1 1
 % Generated by roxygen2: do not edit by hand
2
-% Please edit documentation in R/class-CogapsResult.R
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+% Please edit documentation in R/class-CogapsResult.R, R/methods-CogapsResult.R
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 \docType{methods}
4 4
 \name{computeGeneGSProb}
5 5
 \alias{computeGeneGSProb}
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 \alias{computeGeneGSProb,CogapsResult-method}
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+\alias{computeGeneGSProb}
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 \title{compute gene probability}
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 \usage{
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 computeGeneGSProb(object, GStoGenes, numPerm = 500, Pw = rep(1,
... ...
@@ -39,4 +40,3 @@ data(SimpSim)
39 40
 result <- CoGAPS(SimpSim.D)
40 41
 computeGeneGSProb(result, GSGenes=GSets[[1]], numPerm=500)
41 42
 }
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-
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@@ -23,4 +23,3 @@ back together
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 \details{
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 For file types CoGAPS supports csv, tsv, and mtx
25 25
 }
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-
... ...
@@ -1,9 +1,10 @@
1 1
 % Generated by roxygen2: do not edit by hand
2
-% Please edit documentation in R/class-CogapsResult.R
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+% Please edit documentation in R/class-CogapsResult.R, R/methods-CogapsResult.R
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 \docType{methods}
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 \name{getMeanChiSq}
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 \alias{getMeanChiSq}
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 \alias{getMeanChiSq,CogapsResult-method}
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+\alias{getMeanChiSq}
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 \title{return chi-sq of final matrices}
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 \usage{
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 getMeanChiSq(object)
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@@ -22,4 +23,3 @@ meanChiSq(result)
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 \description{
23 24
 return chi-sq of final matrices
24 25
 }
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-
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@@ -1,9 +1,10 @@
1 1
 % Generated by roxygen2: do not edit by hand
2
-% Please edit documentation in R/class-CogapsParams.R
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+% Please edit documentation in R/class-CogapsParams.R, R/methods-CogapsParams.R
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 \docType{methods}
4 4
 \name{getParam}
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 \alias{getParam}
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 \alias{getParam,CogapsParams-method}
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+\alias{getParam}
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 \title{get the value of a parameter}
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 \usage{
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 getParam(object, whichParam)
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@@ -25,4 +26,3 @@ get the value of a parameter
25 26
  params <- new("CogapsParams")
26 27
  getParam(params, "seed")
27 28
 }
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-
... ...
@@ -13,4 +13,3 @@ initialized CogapsParams object
13 13
 \description{
14 14
 Constructor for CogapsParams
15 15
 }
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-
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@@ -14,4 +14,3 @@ initialized CogapsResult object
14 14
 \description{
15 15
 Constructor for CogapsResult
16 16
 }
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-
... ...
@@ -1,9 +1,10 @@
1 1
 % Generated by roxygen2: do not edit by hand
2
-% Please edit documentation in R/class-CogapsParams.R
2
+% Please edit documentation in R/class-CogapsParams.R, R/methods-CogapsParams.R
3 3
 \docType{methods}
4 4
 \name{parseDirectParams}
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 \alias{parseDirectParams}
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 \alias{parseDirectParams,CogapsParams-method}
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+\alias{parseDirectParams}
7 8
 \title{parse list of parameters passed directly to CoGAPS}
8 9
 \usage{
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 parseDirectParams(object, args)
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@@ -21,4 +22,3 @@ an object of type CogapsParams
21 22
 \description{
22 23
 parse list of parameters passed directly to CoGAPS
23 24
 }
24
-
... ...
@@ -1,9 +1,10 @@
1 1
 % Generated by roxygen2: do not edit by hand
2
-% Please edit documentation in R/class-CogapsParams.R
2
+% Please edit documentation in R/class-CogapsParams.R, R/methods-CogapsParams.R
3 3
 \docType{methods}
4 4
 \name{parseOldParams}
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 \alias{parseOldParams}
6 6
 \alias{parseOldParams,CogapsParams-method}
7
+\alias{parseOldParams}
7 8
 \title{parse list of old-style parameters, store relevant values}
8 9
 \usage{
9 10
 parseOldParams(object, oldArgs)
... ...
@@ -21,4 +22,3 @@ an object of type CogapsParams
21 22
 \description{
22 23
 parse list of old-style parameters, store relevant values
23 24
 }
24
-
... ...
@@ -1,15 +1,15 @@
1 1
 % Generated by roxygen2: do not edit by hand
2
-% Please edit documentation in R/class-CogapsResult.R
2
+% Please edit documentation in R/class-CogapsResult.R, R/methods-CogapsResult.R
3 3
 \docType{methods}
4 4
 \name{patternMarkers}
5 5
 \alias{patternMarkers}
6 6
 \alias{patternMarkers,CogapsResult-method}
7
+\alias{patternMarkers}
7 8
 \title{compute pattern markers statistic}
8 9
 \usage{
9 10
 patternMarkers(object, threshold = "all", lp = NA, full = FALSE)
10 11
 
11
-\S4method{patternMarkers}{CogapsResult}(object, threshold = "all", lp = NA,
12
-  full = FALSE)
12
+\S4method{patternMarkers}{CogapsResult}(object, threshold, lp)
13 13
 }
14 14
 \arguments{
15 15
 \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.}
20 20
 
21 21
 \item{lp}{a vector of weights for each pattern to be used for finding
22 22
 markers. If NA markers for each pattern of the A matrix will be used.}
23
-
24
-\item{full}{logical indicating whether to return the ranks of each gene for
25
-each pattern}
26 23
 }
27 24
 \value{
28 25
 By default a non-overlapping list of genes associated with each
... ...
@@ -32,4 +29,3 @@ for each \code{lp} will also be returned.
32 29
 \description{
33 30
 calculate the most associated pattern for each gene
34 31
 }
35
-
... ...
@@ -30,4 +30,3 @@ consensus pattern is also returned.
30 30
 \description{
31 31
 Match Patterns Across Multiple Runs
32 32
 }
33
-
... ...
@@ -1,18 +1,13 @@
1 1
 % Generated by roxygen2: do not edit by hand
2
-% Please edit documentation in R/class-CogapsResult.R
2
+% Please edit documentation in R/methods-CogapsResult.R
3 3
 \docType{methods}
4 4
 \name{plotPatternMarkers}
5 5
 \alias{plotPatternMarkers}
6
-\alias{plotPatternMarkers,CogapsResult-method}
7 6
 \title{heatmap of original data clustered by pattern markers statistic}
8 7
 \usage{
9 8
 plotPatternMarkers(object, data, patternPalette, sampleNames,
10 9
   samplePalette = NULL, heatmapCol = bluered, colDenogram = TRUE,
11 10
   scale = "row", ...)
12
-
13
-\S4method{plotPatternMarkers}{CogapsResult}(object, data, patternPalette,
14
-  sampleNames, samplePalette = NULL, heatmapCol = bluered,
15
-  colDenogram = TRUE, scale = "row", ...)
16 11
 }
17 12
 \arguments{
18 13
 \item{object}{an object of type CogapsResult}
... ...
@@ -46,4 +41,3 @@ heatmap of original data clustered by pattern markers statistic
46 41
 \seealso{
47 42
 \code{\link{heatmap.2}}
48 43
 }
49
-
... ...
@@ -1,9 +1,10 @@
1 1
 % Generated by roxygen2: do not edit by hand
2
-% Please edit documentation in R/class-CogapsResult.R
2
+% Please edit documentation in R/class-CogapsResult.R, R/methods-CogapsResult.R
3 3
 \docType{methods}
4 4
 \name{plotResiduals}
5 5
 \alias{plotResiduals}
6 6
 \alias{plotResiduals,CogapsResult-method}
7
+\alias{plotResiduals}
7 8
 \title{plot of residuals}
8 9
 \usage{
9 10
 plotResiduals(object, data, uncertainty = NULL)
... ...
@@ -28,4 +29,3 @@ data(SimpSim)
28 29
 result <- CoGAPS(SimpSim.D)
29 30
 plotResiduals(result, SimpSim.D)
30 31
 }
31
-
... ...
@@ -1,9 +1,10 @@
1 1
 % Generated by roxygen2: do not edit by hand
2
-% Please edit documentation in R/class-CogapsResult.R
2
+% Please edit documentation in R/class-CogapsResult.R, R/methods-CogapsResult.R
3 3
 \docType{methods}
4 4
 \name{reconstructGene}
5 5
 \alias{reconstructGene}
6 6
 \alias{reconstructGene,CogapsResult-method}
7
+\alias{reconstructGene}
7 8
 \title{reconstruct gene}
8 9
 \usage{
9 10
 reconstructGene(object, genes = NULL)
... ...
@@ -26,4 +27,3 @@ data(SimpSim)
26 27
 result <- CoGAPS(SimpSim.D)
27 28
 D_estimate <- reconstructGene(result)
28 29
 }
29
-
... ...
@@ -1,9 +1,10 @@
1 1
 % Generated by roxygen2: do not edit by hand
2
-% Please edit documentation in R/class-CogapsParams.R
2
+% Please edit documentation in R/class-CogapsParams.R, R/methods-CogapsParams.R
3 3
 \docType{methods}
4 4
 \name{setParam}
5 5
 \alias{setParam}
6 6
 \alias{setParam,CogapsParams-method}
7
+\alias{setParam}
7 8
 \title{set the value of a parameter}
8 9
 \usage{
9 10
 setParam(object, whichParam, value)
... ...
@@ -27,4 +28,3 @@ set the value of a parameter
27 28
  params <- new("CogapsParams")
28 29
  params <- setParam(params, "seed", 123)
29 30
 }
30
-
... ...
@@ -10,4 +10,3 @@ tf2ugFC
10 10
 \description{
11 11
 Gene sets defined by transcription factors defined from TRANSFAC.
12 12
 }
13
-