![]() I tried to train CTC model based on LibriSpeech dataset,īut CTCLoss always return inf or 0 if I use zero_infinity=True. Object, Amean, Pmean, Asd, Psd, meanChiSq, geneNames, sampleNames, diagnostics = NULL. initial values for slots #' initialized CogapsResult object #' methods callNextMethod #' S4Vectors make_zero_col_DFrame setMethod ( "initialize", "CogapsResult", function (. Object CogapsResult object #' Amean mean of sampled A matrices #' Pmean mean of sampled P matrices #' Asd std dev of sampled A matrices #' Psd std dev of sampled P matrices #' meanChiSq mean value of ChiSq statistic #' geneNames names of genes in data #' sampleNames names of samples in data #' diagnostics assorted diagnostic reports from the run #'. #' CogapsResult #' #' #' factorStdDev std dev of the sampled P matrices #' loadingStdDev std dev of the sampled A matrices #' Contains all output from Cogaps run #' S4Vectors Annotated #' SingleCellExperiment LinearEmbeddingMatrix setClass ( "CogapsResult", contains = "LinearEmbeddingMatrix", slots = c ( factorStdDev = "ANY", # Psd loadingStdDev = "ANY" # Asd )) #' Constructor for CogapsResult #'. ![]() ncolHelper: get number of columns from supported file name or matrix.isRdsFile: checks if file is rds format.initialize-CogapsResult-method: Constructor for CogapsResult.initialize-CogapsParams-method: constructor for CogapsParams.GIST.uncertainty: GIST gene expression uncertainty matrix from Ochs et al.GIST.result: CoGAPS result from running on GIST dataset.GIST.matrix: GIST gene expression data from Ochs et al.GIST.data_frame: GIST gene expression data from Ochs et al.getVersion-methods: return version number used to generate this result.getValueOrRds: get input that might be an RDS file.getUnmatchedPatterns-methods: return unmatched patterns from each subset.getSubsets-methods: return the names of the genes (samples) in each subset.getSampleNames: extract sample names from data.getSampleFactors-methods: return sampleFactors matrix from CogapsResult object.getRetinaSubset: get specified number of retina subsets.getPatternMatrix-methods: return pattern matrix from CogapsResult object.getParam-methods: get the value of a parameter.getOriginalParameters-methods: return original parameters used to generate this result.getMeanChiSq-methods: return chi-sq of final matrices.getGeneNames: extract gene names from data.getFeatureLoadings-methods: return featureLoadings matrix from CogapsResult object.getDimNames: extracts gene/sample names from the data.getCorrelationToMeanPattern-methods: return correlation between each pattern and the cluster mean.getClusteredPatterns-methods: return clustered patterns from set of all patterns across all.getAmplitudeMatrix-methods: return Amplitude matrix from CogapsResult object.findConsensusMatrix: find the consensus pattern matrix across all subsets.distributedCogaps: CoGAPS Distributed Matrix Factorization Algorithm.createSets: partition genes/samples into subsets.createCogapsResult: convert list output from c++ code to a CogapsResult object.corrToMeanPattern: calculate correlation of each pattern in a cluster to the.convertDataToMatrix: convert any acceptable data input to a numeric matrix.computeGeneGSProb-methods: compute gene probability.compiledWithOpenMPSupport: Check if compiler supported OpenMP.CoGAPS-package: CoGAPS: Coordinated Gene Activity in Pattern Sets.CoGAPS: CoGAPS Matrix Factorization Algorithm. ![]()
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