@@ -23,6 +23,7 @@

 #' the fixed patterns

 #' @param fixedPatterns matrix of fixed values in either A or P matrix

 #' @param checkpointInterval time (in seconds) between creating a checkpoint

+#' @param checkpointFile name of the checkpoint file

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

 #' @return list with A and P matrix estimates

 #' @importFrom methods new

@@ -32,8 +33,9 @@

 #' @export

 CoGAPS <- function(D, S, nFactor=7, nEquil=1000, nSample=1000, nOutputs=1000,

 nSnapshots=0, alphaA=0.01, alphaP=0.01, maxGibbmassA=100, maxGibbmassP=100,

-seed=-1, messages=TRUE, singleCellRNASeq=FALSE, whichMatrixFixed = 'N',

-fixedPatterns = matrix(0), checkpointInterval=0, ...)

+seed=-1, messages=TRUE, singleCellRNASeq=FALSE, whichMatrixFixed='N',

+fixedPatterns=matrix(0), checkpointInterval=0, checkpointFile="gaps_checkpoint.out",

+...)

 {

     # get v2 arguments

     oldArgs <- list(...)

@@ -57,12 +59,24 @@ fixedPatterns = matrix(0), checkpointInterval=0, ...)

         stop('D and S must be matrices')

     if (any(D < 0) | any(S < 0))

         stop('D and S matrix must be non-negative')

+    if (nrow(D) != nrow(S) | ncol(D) != ncol(S))

+        stop('D and S matrix have different dimensions')

+    if (whichMatrixFixed == 'A' & nrow(fixedPatterns) != nrow(D))

+        stop('invalid number of rows for fixedPatterns')

+    if (whichMatrixFixed == 'A' & ncol(fixedPatterns) > nFactor)

+        stop('invalid number of columns for fixedPatterns')

+    if (whichMatrixFixed == 'P' & nrow(fixedPatterns) > nFactor)

+        stop('invalid number of rows for fixedPatterns')

+    if (whichMatrixFixed == 'P' & ncol(fixedPatterns) != ncol(D))

+        stop('invalid number of columns for fixedPatterns')

     # run algorithm with call to C++ code

     result <- cogaps_cpp(D, S, nFactor, nEquil, nEquil/10, nSample, nOutputs,

         nSnapshots, alphaA, alphaP, maxGibbmassA, maxGibbmassP, seed, messages,

-        singleCellRNASeq, whichMatrixFixed, fixedPatterns, checkpointInterval)

+        singleCellRNASeq, whichMatrixFixed, fixedPatterns, checkpointInterval,

+        checkpointFile)

+    # label matrices and return list

     patternNames <- paste('Patt', 1:nFactor, sep='')

     rownames(result$Amean) <- rownames(result$Asd) <- rownames(D)

     colnames(result$Amean) <- colnames(result$Asd) <- patternNames

@@ -80,9 +94,9 @@ fixedPatterns = matrix(0), checkpointInterval=0, ...)

 #' @param path path to checkpoint file

 #' @return list with A and P matrix estimates

 #' @export

-CoGapsFromCheckpoint <- function(D, S, path)

+CoGapsFromCheckpoint <- function(D, S, path, checkpointFile="gaps_checkpoint.out")

 {

-    cogapsFromCheckpoint_cpp(D, S, path)

+    cogapsFromCheckpoint_cpp(D, S, path, checkpointFile)

 }

 #' Display Information About Package Compilation

@@ -3,12 +3,10 @@

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

 #' matrix factorization returning the two matrices that reconstruct

 #' the data matrix for whole genome data;

-#' @param D data matrix

-#' @param S uncertainty matrix (std devs for chi-squared of Log Likelihood)

 #' @param nFactor number of patterns (basis vectors, metagenes), which must be

 #' greater than or equal to the number of rows of FP

 #' @param nCores number of cores for parallelization. If left to the default NA, nCores = nSets.

-#' @param Cut number of branches at which to cut dendrogram used in patternMatch4Parallel

+#' @param cut number of branches at which to cut dendrogram used in patternMatch4Parallel

 #' @param minNS minimum of individual set contributions a cluster must contain

 #' @param ... additional parameters to be fed into \code{gapsRun} and \code{gapsMapRun}

 #' @return list of A and P estimates

@@ -21,21 +19,23 @@

 #' @export

 GWCoGAPS <- function(simulationName, nFactor, nCores=NA, cut=NA, minNS=NA, ...)

 {

+    if (!is.null(list(...)$checkpointFile))

+        stop("checkpoint file name automatically set in GWCoGAPS - don't pass this parameter")

     allDataSets <- preInitialPhase(simulationName, nCores)

-    initialResult <- runInitialPhase(allDataSets, nFactor)

-    matchedPatternSets <- postInitialPhase(initialResult, length(allDataSets), cut)

-    finalResult <- runFinalPhase(allDataSets, matchedPatternSets)

-    return(postFinalPhase(allDataSets, matchedPatternSets))

+    initialResult <- runInitialPhase(simulationName, allDataSets, nFactor, ...)

+    matchedPatternSets <- postInitialPhase(initialResult, length(allDataSets), cut, minNS)

+    finalResult <- runFinalPhase(simulationName, allDataSets, matchedPatternSets, ...)

+    return(postFinalPhase(finalResult, matchedPatternSets))

 }

-GWCoGapsFromCheckpoint <- function(simulationName, nCores=NA, cut=NA)

+GWCoGapsFromCheckpoint <- function(simulationName, nCores=NA, cut=NA, minNS=NA, ...)

 {

     allDataSets <- preInitialPhase(simulationName, nCores)

     # figure out phase from file signature

-    initalCpts <- list.files(full.names=TRUE, pattern=paste(simulationName, "_initial_run_*.out"))

-    finalCpts <- list.files(full.names=TRUE, pattern=paste(simulationName, "_final_run_*.out"))

-    cptPrefix <- ifelse(length(finalCpts), "_final_run_", "_initial_run_")

+    initalCpts <- list.files(full.names=TRUE, pattern=paste(simulationName, "_initial_cpt_[0-9]+.out"))

+    finalCpts <- list.files(full.names=TRUE, pattern=paste(simulationName, "_final_cpt_[0-9]+.out"))

+    cptPrefix <- ifelse(length(finalCpts), "_final_cpt_", "_initial_cpt_")

     # run CoGAPS for each set, starting from appropiate checkpoint file

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

@@ -55,8 +55,8 @@ GWCoGapsFromCheckpoint <- function(simulationName, nCores=NA, cut=NA)

     }

     else 

     {

-        matchedPatternSets <- postInitialPhase(result, length(allDataSets), cut)

-        finalResult <- runFinalPhase(allDataSets, matchedPatternSets)

+        matchedPatternSets <- postInitialPhase(result, length(allDataSets), cut, minNS)

+        finalResult <- runFinalPhase(allDataSets, matchedPatternSets, ...)

         return(postFinalPhase(allDataSets, matchedPatternSets))

     }

 }

@@ -64,8 +64,8 @@ GWCoGapsFromCheckpoint <- function(simulationName, nCores=NA, cut=NA)

 preInitialPhase <- function(simulationName, nCores)

 {

     # find data files

-    fileSig <- paste(simulationName, "_partition_*.RData", sep="")

-    allDataSets <- list.files(full.names=TRUE, pattern = fileSig)

+    fileSig <- paste(simulationName, "_partition_[0-9]+.RData", sep="")

+    allDataSets <- list.files(full.names=TRUE, pattern=fileSig)

     # establish the number of cores that we are able to use

     if (is.na(nCores))

@@ -74,7 +74,7 @@ preInitialPhase <- function(simulationName, nCores)

     return(allDataSets)

 }

-runInitialPhase <- function(allDataSets, nFactor)

+runInitialPhase <- function(simulationName, allDataSets, nFactor, ...)

 {

     #generate seeds for parallelization

     nut <- generateSeeds(chains=length(allDataSets), seed=-1)

@@ -87,14 +87,14 @@ runInitialPhase <- function(allDataSets, nFactor)

         sampleD <- sweep(sampleD, 1, apply(sampleD, 1, function(x) pmin(0,min(x))))

         # run CoGAPS without any fixed patterns

-        cptFileName <- paste(simulationName, "_initial_run_", i, ".out", sep="")

+        cptFileName <- paste(simulationName, "_initial_cpt_", i, ".out", sep="")

         CoGAPS(sampleD, sampleS, nFactor=nFactor, seed=nut[i],

             checkpointFile=cptFileName, ...)

     }

     return(initialResult)

 }

-postInitialPhase <- function(initialResult, nSets, cut)

+postInitialPhase <- function(initialResult, nSets, cut, minNS)

 {

     nFactor <- ncol(initialResult[[1]]$Amean)

     BySet <- reOrderBySet(AP=initialResult, nFactor=nFactor, nSets=nSets)

@@ -106,32 +106,34 @@ postInitialPhase <- function(initialResult, nSets, cut)

         minNS=minNS, bySet=TRUE))

 }

-runFinalPhase <- function(allDataSets, matchedPatternSets)

+runFinalPhase <- function(simulationName, allDataSets, matchedPatternSets, ...)

 {

     # generate seeds for parallelization

     nut <- generateSeeds(chains=length(allDataSets), seed=-1)

     # final number of factors

-    nFactorFinal <- dim(matchedPatternSets)[1]

+    nFactorFinal <- nrow(matchedPatternSets[[1]])

     # run fixed CoGAPS

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

+    finalResult <- foreach(i=1:length(allDataSets)) %dopar%

     {

         # load data set and shift values so gene minimum is zero

         load(allDataSets[[i]])

         sampleD <- sweep(sampleD, 1, apply(sampleD, 1, function(x) pmin(0,min(x))))

         # run CoGAPS with fixed patterns

-        cptFileName <- paste(simulationName, "_final_run_", i, ".out", sep="")

-        CoGAPS(sampleD, sampleS, FP=matchedPs, nFactor=nFactorFinal, seed=nut[i],

-            checkpointFile=cptFileName, ...)

+        cptFileName <- paste(simulationName, "_final_cpt_", i, ".out", sep="")

+        CoGAPS(sampleD, sampleS, fixedPatterns=matchedPatternSets[[1]],

+            nFactor=nFactorFinal, seed=nut[i], checkpointFile=cptFileName,

+            whichMatrixFixed='P', ...)

+

     }

     return(finalResult)

 }

 postFinalPhase <- function(finalResult, matchedPatternSets)

 {

-    Aresult <- postFixed4Parallel(finalResult, matchedPatternSets)

+    Aresult <- postFixed4Parallel(finalResult, matchedPatternSets[[1]])

     finalResult <- list("Amean"=Aresult$A, "Asd"=Aresult$Asd,

         "Pmean"=matchedPatternSets, "PbySet"=matchedPatternSets[["PBySet"]])

     class(finalResult) <- append(class(finalResult), "CoGAPS")

@@ -1,12 +1,12 @@

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

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

-cogaps_cpp <- function(D, S, nFactor, nEquil, nEquilCool, nSample, nOutputs, nSnapshots, alphaA, alphaP, maxGibbmassA, maxGibbmassP, seed, messages, singleCellRNASeq, whichMatrixFixed, FP, checkpointInterval) {

-    .Call('_CoGAPS_cogaps_cpp', PACKAGE = 'CoGAPS', D, S, nFactor, nEquil, nEquilCool, nSample, nOutputs, nSnapshots, alphaA, alphaP, maxGibbmassA, maxGibbmassP, seed, messages, singleCellRNASeq, whichMatrixFixed, FP, checkpointInterval)

+cogaps_cpp <- function(D, S, nFactor, nEquil, nEquilCool, nSample, nOutputs, nSnapshots, alphaA, alphaP, maxGibbmassA, maxGibbmassP, seed, messages, singleCellRNASeq, whichMatrixFixed, FP, checkpointInterval, cptFile) {

+    .Call('_CoGAPS_cogaps_cpp', PACKAGE = 'CoGAPS', D, S, nFactor, nEquil, nEquilCool, nSample, nOutputs, nSnapshots, alphaA, alphaP, maxGibbmassA, maxGibbmassP, seed, messages, singleCellRNASeq, whichMatrixFixed, FP, checkpointInterval, cptFile)

 }

-cogapsFromCheckpoint_cpp <- function(D, S, fileName) {

-    .Call('_CoGAPS_cogapsFromCheckpoint_cpp', PACKAGE = 'CoGAPS', D, S, fileName)

+cogapsFromCheckpoint_cpp <- function(D, S, fileName, cptFile) {

+    .Call('_CoGAPS_cogapsFromCheckpoint_cpp', PACKAGE = 'CoGAPS', D, S, fileName, cptFile)

 }

 displayBuildReport_cpp <- function() {

@@ -5,7 +5,7 @@

 #' for gapsMapRun

 #' @return list of two data.frames containing the A matrix estimates or their

 #' corresponding standard deviations from output of parallel CoGAPS

-postFixed4Parallel <- function(AP.fixed=NA, setPs=NA)

+postFixed4Parallel <- function(AP.fixed, setPs)

 {

     ASummary <- do.call(rbind,lapply(AP.fixed, function(x) x$Amean))

     Asd <- do.call(rbind,lapply(AP.fixed, function(x) x$Asd))

@@ -8,7 +8,8 @@ CoGAPS(D, S, nFactor = 7, nEquil = 1000, nSample = 1000,

   nOutputs = 1000, nSnapshots = 0, alphaA = 0.01, alphaP = 0.01,

   maxGibbmassA = 100, maxGibbmassP = 100, seed = -1, messages = TRUE,

   singleCellRNASeq = FALSE, whichMatrixFixed = "N",

-  fixedPatterns = matrix(0), checkpointInterval = 0, ...)

+  fixedPatterns = matrix(0), checkpointInterval = 0,

+  checkpointFile = "gaps_checkpoint.out", ...)

 }

 \arguments{

 \item{D}{data matrix}

@@ -48,6 +49,8 @@ the fixed patterns}

 \item{checkpointInterval}{time (in seconds) between creating a checkpoint}

+\item{checkpointFile}{name of the checkpoint file}

+

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

 }

 \value{

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

 \alias{CoGapsFromCheckpoint}

 \title{Restart CoGAPS from Checkpoint File}

 \usage{

-CoGapsFromCheckpoint(D, S, path)

+CoGapsFromCheckpoint(D, S, path, checkpointFile = "gaps_checkpoint.out")

 }

 \arguments{

 \item{D}{data matrix}

@@ -4,29 +4,15 @@

 \alias{GWCoGAPS}

 \title{GWCoGAPS}

 \usage{

-GWCoGAPS(D, S, nFactor, nSets, nCores = NA, saveBySetResults = FALSE,

-  fname = "GWCoGAPS.AP.fixed", PatternsMatchFN = patternMatch4Parallel,

-  Cut = NA, minNS = NA, ...)

+GWCoGAPS(simulationName, nFactor, nCores = NA, cut = NA, minNS = NA, ...)

 }

 \arguments{

-\item{D}{data matrix}

-

-\item{S}{uncertainty matrix (std devs for chi-squared of Log Likelihood)}

-

 \item{nFactor}{number of patterns (basis vectors, metagenes), which must be

 greater than or equal to the number of rows of FP}

-\item{nSets}{number of sets for parallelization}

-

 \item{nCores}{number of cores for parallelization. If left to the default NA, nCores = nSets.}

-\item{saveBySetResults}{logical indicating whether to save by intermediary by set results. Default is FALSE.}

-

-\item{fname}{character string used to label file output. Default is "GWCoGAPS.AP.fixed"}

-

-\item{PatternsMatchFN}{function to use for pattern matching across sets}

-

-\item{Cut}{number of branches at which to cut dendrogram used in patternMatch4Parallel}

+\item{cut}{number of branches at which to cut dendrogram used in patternMatch4Parallel}

 \item{minNS}{minimum of individual set contributions a cluster must contain}

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

 \alias{postFixed4Parallel}

 \title{Post Processing of Parallel Output}

 \usage{

-postFixed4Parallel(AP.fixed = NA, setPs = NA)

+postFixed4Parallel(AP.fixed, setPs)

 }

 \arguments{

 \item{AP.fixed}{output of parallel gapsMapRun calls with same FP}