@@ -14,15 +14,17 @@ Description: Coordinated Gene Activity in Pattern Sets (CoGAPS)

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

     Thomas D. Sherman <tomsherman159@gmail.com>

 Depends:

-    R (>= 3.5.0),

-    Rcpp

+    R (>= 3.5.0)

 Imports:

     cluster,

+    data.table,

     methods,

     gplots,

     graphics,

+    Rcpp,

     S4Vectors,

-    SingleCellExperiment

+    SingleCellExperiment,

+    SummarizedExperiment

 Suggests:

     testthat,

     knitr,

@@ -2,6 +2,7 @@

 S3method(plot,CogapsResult)

 export(CoGAPS)

+export(GWCoGAPS)

 export(binaryA)

 export(buildReport)

 export(calcCoGAPSStat)

@@ -15,17 +16,40 @@ export(patternMatch)

 export(plotPatternMarkers)

 export(plotResiduals)

 export(reconstructGene)

+export(scCoGAPS)

+export(setDistributedParams)

 export(setParam)

 exportClasses(CogapsParams)

 exportClasses(CogapsResult)

+importClassesFrom(S4Vectors,Annotated)

+importClassesFrom(S4Vectors,character_OR_NULL)

 importClassesFrom(SingleCellExperiment,LinearEmbeddingMatrix)

+importFrom(Rcpp,evalCpp)

+importFrom(SummarizedExperiment,assay)

 importFrom(cluster,agnes)

+importFrom(data.table,fread)

 importFrom(gplots,bluered)

 importFrom(gplots,heatmap.2)

+importFrom(grDevices,colorRampPalette)

+importFrom(grDevices,rainbow)

+importFrom(graphics,legend)

+importFrom(graphics,lines)

+importFrom(graphics,mtext)

 importFrom(graphics,plot)

+importFrom(graphics,points)

+importFrom(methods,"slot<-")

 importFrom(methods,callNextMethod)

+importFrom(methods,is)

 importFrom(methods,new)

+importFrom(methods,slot)

+importFrom(methods,slotNames)

+importFrom(methods,validObject)

+importFrom(stats,as.dist)

 importFrom(stats,as.hclust)

+importFrom(stats,cor)

 importFrom(stats,cutree)

 importFrom(stats,hclust)

+importFrom(stats,runif)

+importFrom(stats,weighted.mean)

+importFrom(tools,file_ext)

 useDynLib(CoGAPS)

@@ -1,22 +1,42 @@

 #' @include class-CogapsParams.R

 NULL

+#' Checks if file is supported

+#' @param file path to file

+#' @return TRUE if file is supported, FALSE if not

+#' @importFrom tools file_ext

+supported <- function(file)

+{

+    if (!is(file, "character"))

+        return(FALSE)

+    return(tools::file_ext(file) %in% c("tsv", "csv", "mtx"))

+}

+

 #' CoGAPS Matrix Factorization Algorithm

 #' @export 

-#' @docType methods

-#' @rdname CoGAPS-methods

 #'

 #' @description calls the C++ MCMC code and performs Bayesian

 #' matrix factorization returning the two matrices that reconstruct

 #' the data matrix

-#' @details For file types CoGAPS supports csv, tsv, and mtx

+#' @details The supported R types are: matrix, data.frame, SummarizedExperiment,

+#' SingleCellExperiment. The supported file types are csv, tsv, and mtx.

 #' @param data File name or R object (see details for supported types)

 #' @param params CogapsParams object

-#' @param uncertainty uncertainty matrix (same supported types as data)

-#' @param fixedMatrix data for fixing the values of either the A or P matrix;

-#'  used in conjuction with whichMatrixFixed (see CogapsParams)

-#' @param checkpointInFile name of the checkpoint file

-#' @param ... keeps backwards compatibility with arguments from older versions

+#' @param nThreads maximum number of threads to run on

+#' @param messages T/F for displaying output

+#' @param outputFrequency number of iterations between each output (set to 0 to

+#' disable status updates, other output is controlled by @code messages)

+#' @param uncertainty uncertainty matrix - either a matrix or a supported

+#' file type

+#' @param checkpointOutFile name of the checkpoint file to create

+#' @param checkpointInterval number of iterations between each checkpoint (set

+#' to 0 to disable checkpoints)

+#' @param checkpointInFile if this is provided, CoGAPS runs from the checkpoint

+#' contained in this file

+#' @param transposeData T/F for transposing data while reading it in - useful

+#' for data that is stored as samples x genes since CoGAPS requires data to be

+#' genes x samples

+#' @param ... allows for overwriting parameters in params

 #' @return CogapsResult object

 #' @examples

 #' # Running from R object

@@ -31,13 +51,14 @@ NULL

 #' params <- new("CogapsParams")

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

 #' resultC <- CoGAPS(GIST.D, params)

-#' @importFrom methods new

+#' @importFrom methods new is

+#' @importFrom SummarizedExperiment assay

 CoGAPS <- function(data, params=new("CogapsParams"), nThreads=NULL,

 messages=TRUE, outputFrequency=500, uncertainty=NULL,

 checkpointOutFile="gaps_checkpoint.out", checkpointInterval=1000,

 checkpointInFile=NULL, transposeData=FALSE, ...)

 {

-    # parse parameters from ...

+    # store all parameters in a list and parse parameters from ...

     allParams <- list("gaps"=params,

         "nThreads"=nThreads,

         "messages"=messages,

@@ -51,54 +72,42 @@ checkpointInFile=NULL, transposeData=FALSE, ...)

     allParams <- parseExtraParams(allParams, list(...))

     # check file extension

-    if (class(data) == "character" & !(file_ext(data) %in% c("tsv", "csv", "mtx")))

+    if (is(data, "character") & !supported(data))

         stop("unsupported file extension for data")

     # check uncertainty matrix

-    if (class(data) == "character" & class(uncertainty) != "character")

+    if (is(data, "character") & !is(uncertainty, "character"))

         stop("uncertainty must be same data type as data (file name)")

-    if (nchar(uncertainty) > 0 & !(file_ext(uncertainty) %in% c("tsv", "csv", "mtx")))

+    if (is(uncertainty, "character") & !supported(uncertainty))

         stop("unsupported file extension for uncertainty")

-

-    # check matrix

-    if (class(uncertainty) != "matrix")

-        stop("uncertainty must be same data type as data (matrix)")

+    if (!is(data, "character") & !is.null(uncertainty) & !is(uncertainty, "matrix"))

+        stop("uncertainty must be a matrix unless data is a file path")

     checkDataMatrix(data, uncertainty, params)

-    # check if uncertainty is null

-    if (is.null(uncertainty) & class(data) == "character")

-        uncertainty <- ""

-    else if (is.null(uncertainty))

-        uncertainty <- matrix(0)

-

     # convert data to matrix

-    if (class(data) == "data.frame")

+    if (is(data, "data.frame"))

         data <- data.matrix(data)

-    else if (class(data) == "SummarizedExperiment")

-        data <- assay(data, "counts")

-    else if (class(data) == "SingleCellExperiment")

-        data <- assay(data, "counts")

+    else if (is(data, "SummarizedExperiment"))

+        data <- SummarizedExperiment::assay(data, "counts")

+    else if (is(data, "SingleCellExperiment"))

+        data <- SummarizedExperiment::assay(data, "counts")

     # determine which function to call cogaps algorithm

-    if (!is.null(callParams$gapsParams@distributed))

+    if (!is.null(allParams$gaps@distributed))

         dispatchFunc <- distributedCogaps # genome-wide or single-cell cogaps

-    else if (class(data) == "character")

-        dispatchFunc <- cogaps_cpp_from_file # data is a file name

+    else if (is(data, "character"))

+        dispatchFunc <- cogaps_cpp_from_file # data is a file path

     else

         dispatchFunc <- cogaps_cpp # default

     # check if we're running from a checkpoint

     if (!is.null(allParams$checkpointInFile))

     {

-        if (!is.null(callParams$gapsParams@distributed))

+        if (!is.null(allParams$gaps@distributed))

             stop("checkpoints not supported for distributed cogaps")

         else

             message("Running CoGAPS from a checkpoint")

     }

-    else

-    {

-        allParams$checkpointInFile <- ""

-    }

     # run cogaps

     gapsReturnList <- dispatchFunc(data, allParams, uncertainty)

@@ -115,6 +124,13 @@ checkpointInFile=NULL, transposeData=FALSE, ...)

     ))

 }

+#' Single Cell CoGAPS

+#' @export

+#'

+#' @description wrapper around single-cell distributed algorithm for CoGAPS

+#' @inheritParams CoGAPS

+#' @return CogapsResult object

+#' @importFrom methods new

 scCoGAPS <- function(data, params=new("CogapsParams"), nThreads=NULL,

 messages=TRUE, outputFrequency=500, uncertainty=NULL,

 checkpointOutFile="gaps_checkpoint.out", checkpointInterval=1000,

@@ -126,6 +142,13 @@ checkpointInFile=NULL, transposeData=FALSE, ...)

         ...)

 }

+#' Genome Wide CoGAPS

+#' @export

+#'

+#' @description wrapper around genome-wide distributed algorithm for CoGAPS

+#' @inheritParams CoGAPS

+#' @return CogapsResult object

+#' @importFrom methods new

 GWCoGAPS <- function(data, params=new("CogapsParams"), nThreads=NULL,

 messages=TRUE, outputFrequency=500, uncertainty=NULL,

 checkpointOutFile="gaps_checkpoint.out", checkpointInterval=1000,

@@ -137,77 +160,37 @@ checkpointInFile=NULL, transposeData=FALSE, ...)

         ...)

 }   

+#' parse parameters passed through the ... variable

+#'

+#' @param allParams list of all parameters

+#' @param extraParams list of parameters in ...

+#' @return allParams with any valid parameters in extraParams added

+#' @note will halt with an error if any parameters in extraParams are invalid

+#' @importFrom methods slotNames

 parseExtraParams <- function(allParams, extraParams)

 {

-

-

-}

-

-#' @rdname parseOldParams-methods

-#' @aliases parseOldParams

-setMethod("parseOldParams", signature(object="CogapsParams"),

-function(object, oldArgs)

-{

-    helper <- function(arg, params, newArg)

-    {

-        if (!is.null(oldArgs[[arg]]))

-        {

-            warning(paste("parameter", arg, "is deprecated, it will still",

-                "work, but setting", newArg, "in the params object is the",

-                "preferred method"))

-            params <- setParam(params, newArg, oldArgs[[arg]])

-            oldArgs[[arg]] <- NULL

-        }            

-        return(params)

-    }

-

-    object <- helper("nFactor", object, "nPatterns")

-    object <- helper("nIter", object, "nIterations")

-    object <- helper("nEquil", object, "nIterations")

-    object <- helper("nSample", object, "nIterations")

-    object <- helper("nOutR", object, "outputFrequency")

-    object <- helper("nOutput", object, "outputFrequency")

-    object <- helper("maxGibbmassA", object, "maxGibbsMassA")

-    object <- helper("max_gibbmass_paraA", object, "maxGibbsMassA")

-    object <- helper("maxGibbmassP", object, "maxGibbsMassP")

-    object <- helper("max_gibbmass_paraP", object, "maxGibbsMassP")

-    object <- helper("singleCellRNASeq", object, "singleCell")

-

-    if (!is.null(oldArgs$nSnapshots) | !is.null(oldArgs$sampleSnapshots) | !is.null(oldArgs$numSnapshots))

-    {

-        warning("snapshots not currently supported in release build")

-        oldArgs$nSnapshots <- NULL

-        oldArgs$sampleSnapshots <- NULL

-        oldArgs$numSnapshots <- NULL

-    }

-    if (!is.null(oldArgs$fixedPatterns))

-        stop("pass fixed matrix in with 'fixedMatrix' argument")

-    if (!is.null(oldArgs$S))

-        stop("pass uncertainty matrix in with 'uncertainty', not 'S'")

-

-    return(object)

-})

-

-#' @rdname parseDirectParams-methods

-#' @aliases parseDirectParams

-setMethod("parseDirectParams", signature(object="CogapsParams"),

-function(object, args)

-{

-    for (s in slotNames(object))

+    # parse direct params

+    for (s in slotNames(allParams$gaps))

     {

-        if (!is.null(args[[s]]))

+        if (!is.null(extraParams[[s]]))

         {

-            object <- setParam(object, s, args[[s]])

+            allParams$gaps <- setParam(allParams$gaps, s, extraParams[[s]])

+            extraParams[[s]] <- NULL

         }

     }

-    return(object)

-})

+    # check for unrecognized options

+    if (length(extraParams) > 0)

+        stop(paste("unrecognized argument:", names(extraParams)[1]))

+

+    return(allParams)

+}

-#' Check that provided data is valid

+#' check that provided data is valid

 #'

 #' @param data data matrix

-#' @param uncertainty uncertainty matrix

+#' @param uncertainty uncertainty matrix, can be null

+#' @param params CogapsParams object

 #' @return throws an error if data has problems

 checkDataMatrix <- function(data, uncertainty, params)

 {

@@ -215,7 +198,7 @@ checkDataMatrix <- function(data, uncertainty, params)

         stop("negative values in data and/or uncertainty matrix")

     if (nrow(data) <= params@nPatterns | ncol(data) <= params@nPatterns)

         stop("nPatterns must be less than dimensions of data")

-    if (sum(dim(uncertainty)) != 2 & sum(uncertainty < 1e-5) > 0)

+    if (sum(uncertainty < 1e-5) > 0)

         warning("small values in uncertainty matrix detected")

 }

@@ -26,7 +26,7 @@ distributedCogaps <- function(data, allParams, uncertainty)

         == "genome-wide", "P", "A")

     # run all subsets with the same fixed matrix

-    finalResult <- foreach(i=1:nSets) %dopar%

+    finalResult <- foreach(i=1:allParams$gaps@nSets) %dopar%

     {

         cogaps_cpp(data, allParams, uncertainty, sets[[i]], consensusMatrix)

     }

@@ -39,6 +39,7 @@ distributedCogaps <- function(data, allParams, uncertainty)

     return(resultList)

 }

+#' @importFrom data.table fread

 nrow_helper <- function(data)

 {

     if (class(data) == "character")

@@ -52,6 +53,7 @@ nrow_helper <- function(data)

     return(nrow(data))

 }

+#' @importFrom data.table fread

 ncol_helper <- function(data)

 {

     if (class(data) == "character")

@@ -108,6 +110,7 @@ findConsensusMatrix <- function(result, allParams)

 #' @param ... additional parameters for \code{agnes}

 #' @return a matrix of consensus patterns by samples. If \code{bySet=TRUE} then a list of the set contributions to each

 #' consensus pattern is also returned.

+#' @importFrom stats weighted.mean

 patternMatch <- function(allPatterns, allParams)

 {

     cc <- corcut(allPatterns, allParams)

@@ -138,7 +141,7 @@ patternMatch <- function(allPatterns, allParams)

 }

 #' @importFrom cluster agnes

-#' @importFrom stats cutree as.hclust

+#' @importFrom stats cutree as.hclust cor

 corcut <- function(allPatterns, allParams)

 {

     corr.dist <- cor(allPatterns)

@@ -21,6 +21,7 @@

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

 #' @docType package

 #' @name CoGAPS-package

+#' @importFrom Rcpp evalCpp

 #' @useDynLib CoGAPS

 NULL

@@ -1,11 +1,11 @@

 # Generated by using Rcpp::compileAttributes() -> do not edit by hand

 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

-cogaps_cpp_from_file <- function(data, allParams, uncertainty, indices = numericVector(1), fixedMatrix = matrix(1,1)) {

+cogaps_cpp_from_file <- function(data, allParams, uncertainty, indices = NULL, fixedMatrix = NULL) {

     .Call('_CoGAPS_cogaps_cpp_from_file', PACKAGE = 'CoGAPS', data, allParams, uncertainty, indices, fixedMatrix)

 }

-cogaps_cpp <- function(data, allParams, uncertainty, indices = numericVector(1), fixedMatrix = matrix(1,1)) {

+cogaps_cpp <- function(data, allParams, uncertainty, indices = NULL, fixedMatrix = NULL) {

     .Call('_CoGAPS_cogaps_cpp', PACKAGE = 'CoGAPS', data, allParams, uncertainty, indices, fixedMatrix)

 }

@@ -20,6 +20,7 @@

 #' a cluster must contain

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

 #' a cluster can contain

+#' @importClassesFrom S4Vectors character_OR_NULL

 setClass("CogapsParams", slots = c(

     nPatterns = "numeric",

     nIterations = "numeric",

@@ -29,9 +30,9 @@ setClass("CogapsParams", slots = c(

     maxGibbsMassP = "numeric",

     seed = "numeric",

     singleCell = "logical",

-    distributed = "character",

-    cut = "numeric",

+    distributed = "character_OR_NULL",

     nSets = "numeric",

+    cut = "numeric",

     minNS = "numeric",

     maxNS = "numeric"

 ))

@@ -51,9 +52,9 @@ setMethod("initialize", "CogapsParams",

         .Object@maxGibbsMassP <- 100

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

         .Object@singleCell <- FALSE

-        .Object@distributed <- ""

+        .Object@distributed <- NULL

         .Object@cut <- .Object@nPatterns

-        .Object@nSets <- 3

+        .Object@nSets <- 4

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

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

@@ -62,7 +63,7 @@ setMethod("initialize", "CogapsParams",

     }

 )

-#' defines a valid parameters object

+## defines a valid parameters object

 setValidity("CogapsParams",

     function(object)

     {

@@ -70,20 +71,12 @@ setValidity("CogapsParams",

             "number of patterns must be an integer greater than zero"

         if (object@nIterations <= 0 | object@nIterations %% 1 != 0)

             "number of iterations must be an integer greater than zero"

-        if (object@outputFrequency <= 0 | object@outputFrequency %% 1 != 0)

-            "the output frequency must be an integer greater than zero"

         if (object@alphaA  <= 0 | object@alphaP <= 0)

             "alpha parameter must be greater than zero"

         if (object@maxGibbsMassA  <= 0 | object@maxGibbsMassP <= 0)

             "maxGibbsMass must be greater than zero"

         if (object@seed <= 0 | object@seed %% 1 != 0)

             "random seed must be an integer greater than zero"

-        if (!(object@whichMatrixFixed %in% c("N", "A", "P")))

-            "whichMatrixFixed must be either A or P (N in the case of neither)"

-        if (object@checkpointInterval <= 0 | object@checkpointInterval %% 1 != 0)

-            "checkpointInterval must be an integer greater than zero"

-        if (object@nCores <= 0 | object@nCores %% 1 != 0)

-            "number of cores must be an integer greater than zero"

         if (object@minNS <= 1 | object@minNS %% 1 != 0)

             "minNS must be an integer greater than one"

     }

@@ -104,6 +97,24 @@ setValidity("CogapsParams",

 setGeneric("setParam", function(object, whichParam, value)

     {standardGeneric("setParam")})

+#' set the value of parameters for distributed CoGAPS

+#' @export

+#' @docType methods

+#' @rdname setDistributedParams-methods

+#'

+#' @description these parameters  are interrelated so they must be set together

+#' @param object an object of type CogapsParams

+#' @param cut a distributed CoGAPS parameter 

+#' @param minNS a distributed CoGAPS parameter 

+#' @param maxNS a distributed CoGAPS parameter 

+#' @return the modified params object

+#' @examples

+#'  params <- new("CogapsParams")

+#'  params <- setDistributedParams(3, 2, 4)

+setGeneric("setDistributedParams", function(object, cut=NULL,

+minNS=NULL, maxNS=NULL)

+    {standardGeneric("setDistributedParams")})

+

 #' get the value of a parameter

 #' @export

 #' @docType methods

@@ -2,6 +2,7 @@

 #' @export

 #'

 #' @description Contains all output from Cogaps run

+#' @importClassesFrom S4Vectors Annotated

 #' @importClassesFrom SingleCellExperiment LinearEmbeddingMatrix

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

     sampleStdDev = "ANY",   # Psd transpose

@@ -152,7 +153,7 @@ setGeneric("calcCoGAPSStat", function(object, GStoGenes, numPerm=500)

 #' listed in a gene set behaves like other genes in the set within

 #' the given data set

 #' @param object an object of type CogapsResult

-#' @param GSGenes data.frame or list with gene sets

+#' @param GStoGenes data.frame or list with gene sets

 #' @param numPerm number of permutations for null

 #' @param Pw weight on genes

 #' @param nullGenes logical indicating gene adjustment

@@ -162,7 +163,7 @@ setGeneric("calcCoGAPSStat", function(object, GStoGenes, numPerm=500)

 #' result <- CoGAPS(SimpSim.D)

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

 setGeneric("calcGeneGSStat", function(object, GStoGenes, numPerm,

-Pw=rep(1,ncol(Amean)), nullGenes=FALSE)

+Pw=rep(1,ncol(object@featureLoadings)), nullGenes=FALSE)

     {standardGeneric("calcGeneGSStat")})

 #' compute gene probability

@@ -176,7 +177,7 @@ Pw=rep(1,ncol(Amean)), nullGenes=FALSE)

 #' comparing the inferred activity of that gene to the average activity of the

 #' set.

 #' @param object an object of type CogapsResult

-#' @param GSGenes data.frame or list with gene sets

+#' @param GStoGenes data.frame or list with gene sets

 #' @param Pw weight on genes

 #' @param numPerm number of permutations for null

 #' @param PwNull - logical indicating gene adjustment

@@ -187,7 +188,7 @@ Pw=rep(1,ncol(Amean)), nullGenes=FALSE)

 #' result <- CoGAPS(SimpSim.D)

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

 setGeneric("computeGeneGSProb", function(object, GStoGenes, numPerm=500,

-Pw=rep(1,ncol(Amean)), PwNull=FALSE)

+Pw=rep(1,ncol(object@featureLoadings)), PwNull=FALSE)

     {standardGeneric("computeGeneGSProb")})

 #' compute pattern markers statistic

@@ -2,27 +2,93 @@ 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")

+    cat("\n")

+    cat("-- Standard Parameters --\n")

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

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

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

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

+    cat("distributed   ", ifelse(is.null(object@distributed), FALSE, TRUE), "\n")

+    cat("\n")

+    cat("-- Sparsity Parameters --\n")

+    if (object@alphaA == object@alphaP)

+    {

+        cat("alpha         ", object@alphaA, "\n")

+    }

+    else

+    {

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

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

+    }

+

+    if (object@maxGibbsMassA == object@maxGibbsMassP)

+    {

+        cat("maxGibbsMass  ", object@maxGibbsMassA, "\n")

+    }

+    else

+    {

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

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

+    }

+    if (!is.null(object@distributed))

+    {

+        cat("\n")

+        cat("-- Distributed CoGAPS Parameters --", "\n")

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

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

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

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

+    }

 })

 #' @rdname setParam-methods

 #' @aliases setParam

+#' @importFrom methods slot slot<- validObject

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

 function(object, whichParam, value)

 {

-    slot(object, whichParam) <- value

+    if (whichParam == "alpha")

+    {

+        object@alphaA <- value

+        object@alphaP <- value

+    }

+    else if (whichParam == "maxGibbsMass")

+    {

+        object@maxGibbsMassA <- value

+        object@maxGibbsMassP <- value

+    }

+    else if (whichParam %in% c("cut", "minNS", "maxNS"))

+    {

+        stop("please set this parameter with setDistributedParams")

+    }

+    else

+    {

+        slot(object, whichParam) <- value

+    }

     validObject(object)

     return(object)

 })

+#' @rdname setDistributedParams-methods

+#' @aliases setDistributedParams

+#' @importFrom methods slot

+setMethod("setDistributedParams", signature(object="CogapsParams"),

+function(object, cut, minNS, maxNS)

+{

+    object@cut <- cut

+    object@minNS <- minNS

+    object@maxNS <- maxNS

+

+    if (is.null(object@cut))

+        object@cut <- object@nPatterns

+    if (is.null(object@minNS))

+        object@minNS <- ceiling(object@nSets / 2)

+    if (is.null(object@maxNS))

+        object@maxNS <- object@minNS + object@nSets

+

+    return(object)

+})

+

 #' @rdname getParam-methods

 #' @aliases getParam

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

@@ -11,7 +11,8 @@ function(object)

 })

 #' @export

-#' @importFrom graphics plot

+#' @importFrom graphics plot legend lines points

+#' @importFrom grDevices rainbow

 plot.CogapsResult <- function(x, ...)

 {

     nSamples <- nrow(object@sampleFactors)

@@ -75,6 +76,7 @@ function(object, genes)

 #' @rdname binaryA-methods

 #' @aliases binaryA

 #' @importFrom gplots heatmap.2

+#' @importFrom graphics mtext

 setMethod("binaryA", signature(object="CogapsResult"),

 function(object, threshold)

 {

@@ -92,6 +94,7 @@ function(object, threshold)

 #' @rdname plotResiduals-methods

 #' @aliases plotResiduals

 #' @importFrom gplots heatmap.2

+#' @importFrom grDevices colorRampPalette

 setMethod("plotResiduals", signature(object="CogapsResult"),

 function(object, data, uncertainty)

 {

@@ -194,7 +197,7 @@ function(object, threshold, lp)

 #' @seealso  \code{\link{heatmap.2}}

 #' @importFrom gplots bluered

 #' @importFrom gplots heatmap.2

-#' @importFrom stats hclust

+#' @importFrom stats hclust as.dist cor

 plotPatternMarkers <- function(object, data, patternPalette, sampleNames,

 samplePalette=NULL, heatmapCol=bluered, colDenogram=TRUE, scale="row", ...)

 {

@@ -229,6 +232,8 @@ samplePalette=NULL, heatmapCol=bluered, colDenogram=TRUE, scale="row", ...)

 #' @rdname calcCoGAPSStat-methods

 #' @aliases calcCoGAPSStat

+#' @importFrom stats runif

+#' @importFrom methods is

 setMethod("calcCoGAPSStat", signature(object="CogapsResult"),

 function(object, GStoGenes, numPerm)

 {

@@ -346,7 +351,7 @@ function(object, GStoGenes, numPerm)

 setMethod("calcGeneGSStat", signature(object="CogapsResult"),

 function(object, GStoGenes, numPerm, Pw, nullGenes)

 {

-    gsStat <- calcCoGAPSStat(object, data.frame(GSGenes), numPerm=numPerm)

+    gsStat <- calcCoGAPSStat(object, data.frame(GStoGenes), numPerm=numPerm)

     gsStat <- gsStat$GSUpreg

     gsStat <- -log(gsStat)

@@ -361,12 +366,12 @@ function(object, GStoGenes, numPerm, Pw, nullGenes)

     if (nullGenes)

     {

-        ZD <- object@featureLoadings[setdiff(row.names(object@featureLoadings), GSGenes),] /

-            object@featureStdDev[setdiff(row.names(object@featureLoadings), GSGenes),]

+        ZD <- object@featureLoadings[setdiff(row.names(object@featureLoadings), GStoGenes),] /

+            object@featureStdDev[setdiff(row.names(object@featureLoadings), GStoGenes),]

     }

     else

     {

-        ZD <- object@featureLoadings[GSGenes,]/object@featureStdDev[GSGenes,]

+        ZD <- object@featureLoadings[GStoGenes,]/object@featureStdDev[GStoGenes,]

     }

     outStats <- apply(sweep(ZD,2,gsStat,FUN="*"),1,sum) / (sum(gsStat))

     outStats <- outStats / apply(ZD,1,sum)

@@ -384,21 +389,21 @@ function(object, GStoGenes, numPerm, Pw, nullGenes)

 setMethod("computeGeneGSProb", signature(object="CogapsResult"),

 function(object, GStoGenes, numPerm, Pw, PwNull)

 {

-    geneGSStat <- calcGeneGSStat(object, Pw=Pw, GSGenes=GSGenes,

+    geneGSStat <- calcGeneGSStat(object, Pw=Pw, GStoGenes=GStoGenes,

         numPerm=numPerm)

     if (PwNull)

     {

-        permGSStat <- calcGeneGSStat(object, GSGenes=GSGenes, numPerm=numPerm,

+        permGSStat <- calcGeneGSStat(object, GStoGenes=GStoGenes, numPerm=numPerm,

             Pw=Pw, nullGenes=TRUE)

     }

     else

     {

-        permGSStat <- calcGeneGSStat(object, GSGenes=GSGenes, numPerm=numPerm,

+        permGSStat <- calcGeneGSStat(object, GStoGenes=GStoGenes, numPerm=numPerm,

             nullGenes=TRUE)

     }

-    finalStats <- sapply(GSGenes, function(x)

+    finalStats <- sapply(GStoGenes, function(x)

         length(which(permGSStat > geneGSStat[x])) / length(permGSStat))

     return(finalStats)

similarity index 52%

rename from man/CoGAPS-methods.Rd

rename to man/CoGAPS.Rd

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

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/CoGAPS.R

-\docType{methods}

 \name{CoGAPS}

 \alias{CoGAPS}

 \title{CoGAPS Matrix Factorization Algorithm}

@@ -15,14 +14,29 @@ CoGAPS(data, params = new("CogapsParams"), nThreads = NULL,

 \item{params}{CogapsParams object}

-\item{uncertainty}{uncertainty matrix (same supported types as data)}

+\item{nThreads}{maximum number of threads to run on}

-\item{checkpointInFile}{name of the checkpoint file}

+\item{messages}{T/F for displaying output}

-\item{...}{keeps backwards compatibility with arguments from older versions}

+\item{outputFrequency}{number of iterations between each output (set to 0 to

+disable status updates, other output is controlled by @code messages)}

-\item{fixedMatrix}{data for fixing the values of either the A or P matrix;

-used in conjuction with whichMatrixFixed (see CogapsParams)}

+\item{uncertainty}{uncertainty matrix - either a matrix or a supported

+file type}

+

+\item{checkpointOutFile}{name of the checkpoint file to create}

+

+\item{checkpointInterval}{number of iterations between each checkpoint (set

+to 0 to disable checkpoints)}

+

+\item{checkpointInFile}{if this is provided, CoGAPS runs from the checkpoint

+contained in this file}

+

+\item{transposeData}{T/F for transposing data while reading it in - useful

+for data that is stored as samples x genes since CoGAPS requires data to be

+genes x samples}

+

+\item{...}{allows for overwriting parameters in params}

 }

 \value{

 CogapsResult object

@@ -33,7 +47,8 @@ matrix factorization returning the two matrices that reconstruct

 the data matrix

 }

 \details{

-For file types CoGAPS supports csv, tsv, and mtx

+The supported R types are: matrix, data.frame, SummarizedExperiment,

+SingleCellExperiment. The supported file types are csv, tsv, and mtx.

 }

 \examples{

 # Running from R object

new file mode 100644

@@ -0,0 +1,46 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/CoGAPS.R

+\name{GWCoGAPS}

+\alias{GWCoGAPS}

+\title{Genome Wide CoGAPS}

+\usage{

+GWCoGAPS(data, params = new("CogapsParams"), nThreads = NULL,

+  messages = TRUE, outputFrequency = 500, uncertainty = NULL,

+  checkpointOutFile = "gaps_checkpoint.out", checkpointInterval = 1000,

+  checkpointInFile = NULL, transposeData = FALSE, ...)

+}

+\arguments{

+\item{data}{File name or R object (see details for supported types)}

+

+\item{params}{CogapsParams object}

+

+\item{nThreads}{maximum number of threads to run on}

+

+\item{messages}{T/F for displaying output}

+

+\item{outputFrequency}{number of iterations between each output (set to 0 to

+disable status updates, other output is controlled by @code messages)}

+

+\item{uncertainty}{uncertainty matrix - either a matrix or a supported

+file type}

+

+\item{checkpointOutFile}{name of the checkpoint file to create}

+

+\item{checkpointInterval}{number of iterations between each checkpoint (set

+to 0 to disable checkpoints)}

+

+\item{checkpointInFile}{if this is provided, CoGAPS runs from the checkpoint

+contained in this file}

+

+\item{transposeData}{T/F for transposing data while reading it in - useful

+for data that is stored as samples x genes since CoGAPS requires data to be

+genes x samples}

+

+\item{...}{allows for overwriting parameters in params}

+}

+\value{

+CogapsResult object

+}

+\description{

+wrapper around genome-wide distributed algorithm for CoGAPS

+}

@@ -7,22 +7,22 @@

 \alias{calcGeneGSStat}

 \title{probability gene belongs in gene set}

 \usage{

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

-  nullGenes = FALSE)

+calcGeneGSStat(object, GStoGenes, numPerm, Pw = rep(1,

+  ncol(object@featureLoadings)), nullGenes = FALSE)

 \S4method{calcGeneGSStat}{CogapsResult}(object, GStoGenes, numPerm,

-  Pw = rep(1, ncol(Amean)), nullGenes = FALSE)

+  Pw = rep(1, ncol(object@featureLoadings)), nullGenes = FALSE)

 }

 \arguments{

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

+\item{GStoGenes}{data.frame or list with gene sets}

+

 \item{numPerm}{number of permutations for null}

 \item{Pw}{weight on genes}

 \item{nullGenes}{logical indicating gene adjustment}

-

-\item{GSGenes}{data.frame or list with gene sets}

 }

 \value{

 gene similiarity statistic

@@ -2,18 +2,20 @@