Former-commit-id: 3916a9874ea8b506ed6e9270a56d47a0696a9371
Sean Corbett authored on 03/12/2018 21:18:30
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@@ -1,5 +1,74 @@ |
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# Generated by roxygen2: do not edit by hand |
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+export("completeLogLik<-")
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+export("countChecksum<-")
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+export("finalLogLik<-")
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+export("initialSeed<-")
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+export("matrixNames<-")
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+export("resList<-")
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+export("runParams<-")
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+export("sampleLabel<-")
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+export("setPerplexity<-")
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+export(DeconX) |
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+export(available_models) |
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+export(celda) |
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+export(celdaGridSearch) |
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+export(celdaHeatmap) |
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+export(celdaProbabilityMap) |
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+export(celdaTsne) |
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+export(celda_C) |
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+export(celda_CG) |
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+export(celda_G) |
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+export(clusterProbability) |
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+export(compareCountMatrix) |
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+export(completeLogLik) |
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+export(countChecksum) |
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+export(differentialExpression) |
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+export(distinct_colors) |
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+export(factorizeMatrix) |
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+export(featureModuleLookup) |
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+export(finalLogLik) |
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+export(getPerplexity) |
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+export(initialSeed) |
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+export(logLikelihood) |
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+export(logLikelihood.celda_C) |
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+export(logLikelihood.celda_CG) |
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+export(logLikelihood.celda_G) |
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+export(matrixNames) |
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+export(moduleHeatmap) |
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+export(normalizeCounts) |
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+export(perplexity) |
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+export(plotDimReduceCluster) |
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+export(plotDimReduceFeature) |
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+export(plotDimReduceGrid) |
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+export(plotDimReduceModule) |
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+export(plotGridSearchPerplexity) |
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+export(plotGridSearchPerplexity.celda_C) |
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+export(plotGridSearchPerplexity.celda_CG) |
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+export(plotGridSearchPerplexity.celda_G) |
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+export(plotHeatmap) |
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+export(recodeClusterY) |
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+export(recodeClusterZ) |
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+export(resList) |
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+export(resamplePerplexity) |
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+export(runParams) |
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+export(sampleLabel) |
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+export(selectBestModel) |
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+export(semi_pheatmap) |
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+export(simulateCells) |
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+export(simulateCells.celda_C) |
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+export(simulateCells.celda_CG) |
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+export(simulateCells.celda_G) |
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+export(simulateObservedMatrix) |
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+export(subsetCeldaList) |
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+export(topRank) |
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+exportMethods(celdaHeatmap) |
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+exportMethods(celdaProbabilityMap) |
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+exportMethods(celdaTsne) |
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+exportMethods(clusterProbability) |
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+exportMethods(factorizeMatrix) |
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+exportMethods(featureModuleLookup) |
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+exportMethods(perplexity) |
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import(RColorBrewer) |
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import(data.table) |
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import(foreach) |
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@@ -29,7 +29,7 @@ |
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#' @title celda.CG.grid.search.res |
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#' @format An object as returned from celdaGridSearch() |
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#' @examples |
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-#' cgs = celdaGridSearch(celda.CG.sim$counts, model="celda_CG", |
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+#' cgs = celda::celdaGridSearch(celda.CG.sim$counts, model="celda_CG", |
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#' params.test=list(K=4:6, L=9:11), |
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#' params.fixed=list(sample.label=celda.CG.sim$sample.label), |
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#' best.only=TRUE, nchains=1) |
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@@ -12,7 +12,7 @@ celda.CG.grid.search.res |
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Example results of celdaGridSearch on celda.CG.sim |
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} |
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\examples{
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-cgs = celdaGridSearch(celda.CG.sim$counts, model="celda_CG", |
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+cgs = celda::celdaGridSearch(celda.CG.sim$counts, model="celda_CG", |
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params.test=list(K=4:6, L=9:11), |
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params.fixed=list(sample.label=celda.CG.sim$sample.label), |
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best.only=TRUE, nchains=1) |
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@@ -81,5 +81,5 @@ list A list containing dendrogram information and the heatmap grob |
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Renders a heatmap based on a matrix of counts where rows are features and columns are cells. |
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} |
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\examples{
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-plotHeatmap(celda.CG.sim$counts, z=celda.CG.mod@z, y=celda.CG.mod@y) |
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+plotHeatmap(celda.CG.sim$counts, z=clustering(celda.CG.mod)$z, y=clustering(celda.CG.mod)$y) |
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} |