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"GetDetailedNbPeptides", "title": "Computes the detailed number of peptides for each protein", "topics": [ "GetDetailedNbPeptides" ] }, { "page": "GetDetailedNbPeptidesUsed", "title": "Computes the detailed number of peptides used for aggregating each protein", "topics": [ "GetDetailedNbPeptidesUsed" ] }, { "page": "GetHistory", "title": "Wrapper for the 'paramshistory' function.", "topics": [ "GetHistory" ] }, { "page": "GetIndices_BasedOnConditions", "title": "Search lines which respects request on one or more conditions.", "topics": [ "GetIndices_BasedOnConditions" ] }, { "page": "GetIndices_FunFiltering", "title": "Delete the lines in the matrix of intensities and the metadata table given their indices.", "topics": [ "GetIndices_FunFiltering" ] }, { "page": "GetIndices_WholeLine", "title": "Search lines which respects query on all their elements.", "topics": [ "GetIndices_WholeLine" ] }, { "page": "GetIndices_WholeMatrix", "title": "Search lines which respects request on one or more conditions.", "topics": [ "GetIndices_WholeMatrix" ] }, { "page": "getListNbValuesInLines", "title": "Returns the possible number of values in lines in the data", "topics": [ "getListNbValuesInLines" ] }, { "page": "GetNbPeptidesUsed", "title": "Computes the number of peptides used for aggregating each protein", "topics": [ "GetNbPeptidesUsed" ] }, { "page": "GetNbTags", "title": "Number of each metacell tags", "topics": [ "GetNbTags" ] }, { "page": "getNumberOfEmptyLines", "title": "Returns the number of empty lines in the data", "topics": [ "getNumberOfEmptyLines" ] }, { "page": "getPepProtCC", "title": "Build the list of connex composant of the adjacency matrix", "topics": [ "getPepProtCC" ] }, { "page": "getProteinsStats", "title": "Computes the number of proteins that are only defined by specific peptides, shared peptides or a mixture of two.", "topics": [ "getProteinsStats" ] }, { "page": "GetSoftAvailables", "title": "The set of available softwares to convert from", "topics": [ "GetSoftAvailables" ] }, { "page": "globalAdjPval", "title": "Computes the adjusted p-values on all the stacked contrasts using CP4P", "topics": [ "globalAdjPval" ] }, { "page": "GraphPepProt", "title": "Function to create a histogram that shows the repartition of peptides w.r.t. the proteins", "topics": [ "GraphPepProt" ] }, { "page": "hc_logFC_DensityPlot", "title": "Density plots of logFC values", "topics": [ "hc_logFC_DensityPlot" ] }, { "page": "heatmap", "title": "Display a heatmap for data with missing values", "topics": [ "heatmapForMissingValues" ] }, { "page": "histPValue_HC", "title": "Plots a histogram of p-values", "topics": [ "histPValue_HC" ] }, { "page": "imputePA2", "title": "Missing values imputation from a 'MSnSet' object", "topics": [ "imputePA2" ] }, { "page": "InitializeHistory", "title": "Initialize the history", "topics": [ "InitializeHistory" ] }, { "page": "isDifferential", "title": "Identification of differentially abundant peptide/protein", "topics": [ "isDifferential" ] }, { "page": "isOfType", "title": "Similar to the function 'is.na()' but focused on the equality with the paramter 'type'.", "topics": [ "isOfType" ] }, { "page": "isSubset", "title": "Check is a given set is a subset of another one.", "topics": [ "isSubset" ] }, { "page": "Keep_Items_from_Dataset", "title": "Removes assay from a 'QFeatures' object", "topics": [ "Keep_Items_from_Dataset" ] }, { "page": "LH0", "title": "Compute the likelihood of the null hypothesis for the global model", "topics": [ "LH0" ] }, { "page": "LH0_lm", "title": "Compute the likelihoods of the null hypothesis for the \"local\" component-wise model", "topics": [ "LH0_lm" ] }, { "page": "LH1", "title": "Compute the likelihood of the alternative hypothesis for the global model", "topics": [ "LH1" ] }, { "page": "LH1_lm", "title": "Compute the likelihoods of the alternative hypothesis for the \"local\" component-wise model", "topics": [ "LH1_lm" ] }, { "page": "limmaCompleteTest", "title": "Computes a hierarchical differential analysis", "topics": [ "limmaCompleteTest" ] }, { "page": "makeContrast", "title": "Builds the contrast matrix", "topics": [ "makeContrast" ] }, { "page": "makeDesign", "title": "Builds the design matrix", "topics": [ "makeDesign" ] }, { "page": "makeDesign1", "title": "Builds the design matrix for designs of level 1", "topics": [ "makeDesign1" ] }, { "page": "makeDesign2", "title": "Builds the design matrix for designs of level 2", "topics": [ "makeDesign2" ] }, { "page": "makeDesign3", "title": "Builds the design matrix for designs of level 3", "topics": [ "makeDesign3" ] }, { "page": "matchMetacell", "title": "Similar to the function 'is.na()' but focused on the equality with the paramter 'type'.", "topics": [ "matchMetacell" ] }, { "page": "Metacell_DIA_NN", "title": "Sets the metacell dataframe for datasets which are from Dia-NN software", "topics": [ "Metacell_DIA_NN" ] }, { "page": "Metacell_maxquant", "title": "Sets the metacell dataframe", "topics": [ "Metacell_maxquant" ] }, { "page": "Metacell_proline", "title": "Sets the metacell dataframe for datasets which are from Proline software", "topics": [ "Metacell_proline" ] }, { "page": "metacell-plots", "title": "Bar plot of missing values per lines using plotly", "topics": [ "hc_mvTypePlot2", "metacell-plots", "metacellHisto_HC", "metacellPerLinesHistoPerCondition_HC", "metacellPerLinesHisto_HC", "mvImage", "wrapperMVImage" ] }, { "page": "MetacellFilteringScope", "title": "Lists the metacell scopes for filtering", "topics": [ "MetacellFilteringScope" ] }, { "page": "mv_imputation_protein", "title": "Finds the LAPALA", "topics": [ "findMECBlock", "getQuantile4Imp", "mv_imputation_protein", "reIntroduceMEC", "wrapperImputeDetQuant", "wrapperImputeFixedValue", "wrapperImputeKNN", "wrapperImputePA", "wrapperImputeSLSA" ] }, { "page": "NAIsZero", "title": "Set NA values to 0", "topics": [ "NAIsZero" ] }, { "page": "nEmptyLines", "title": "Number of empty lines in the data", "topics": [ "nEmptyLines" ] }, { "page": "nonzero", "title": "Retrieve the indices of non-zero elements in sparse matrices", "topics": [ "nonzero" ] }, { "page": "normalization_methods", "title": "Normalisation", "topics": [ "GlobalQuantileAlignment", "LOESS", "MeanCentering", "normalization_methods", "normalizeMethods", "QuantileCentering", "SumByColumns", "vsn" ] }, { "page": "normalizeFunction", "title": "Normalisation for QFeatures", "topics": [ "normalizeFunction" ] }, { "page": "output_2_Excel", "title": "This function exports a data.frame to a Excel file.", "topics": [ "listSheets", "output_2_Excel", "readExcel", "writeExcel", "WriteHistory", "write_Assay_To_Excel", "Write_RowData", "Write_SamplesData_to_Excel" ] }, { "page": "OWAnova", "title": "Applies aov() on a vector of protein abundances using the design derived from the sample names (simple aov wrapper)", "topics": [ "OWAnova" ] }, { "page": "QFeatures-accessors", "title": "List of metacell tags", "topics": [ "analysis", "analysis,QFeatures-method", "analysis,SummarizedExperiment-method", "analysis<-", "ConnectedComp", "ConnectedComp,QFeatures-method", "ConnectedComp,SummarizedExperiment-method", "ConnectedComp<-", "design_qf", "design_qf,QFeatures-method", "design_qf<-", "DifferentialAnalysis", "DifferentialAnalysis,QFeatures-method", "DifferentialAnalysis,SummarizedExperiment-method", "DifferentialAnalysis<-", "filename", "filename,QFeatures-method", "filename<-", "GetMetacellTags", "GetMetacellTags,data.frame-method", "GetMetacellTags,QFeatures-method", "GetMetacellTags,SummarizedExperiment-method", "GetMetadataSlot", "GetRowdataSlot", "GetUniqueTags", "GetUniqueTags,QFeatures-method", "GetUniqueTags,SummarizedExperiment-method", "HypothesisTest", "HypothesisTest,QFeatures-method", "HypothesisTest,SummarizedExperiment-method", "HypothesisTest<-", "idcol", "idcol,QFeatures-method", "idcol,SummarizedExperiment-method", "idcol<-", "mainAssay", "names_metacell", "names_metacell,QFeatures-method", "names_metacell,SummarizedExperiment-method", "names_metacell<-", "paramshistory", "paramshistory,QFeatures-method", "paramshistory,SummarizedExperiment-method", "paramshistory<-", "parentProtId", "parentProtId,QFeatures-method", "parentProtId,SummarizedExperiment-method", "parentProtId<-", "QFeatures-accessors", "qMetacell", "qMetacell,QFeatures-method", "qMetacell,SummarizedExperiment-method", "qMetacell<-", "typeDataset", "typeDataset,QFeatures-method", "typeDataset,SummarizedExperiment-method", "typeDataset<-", "version", "version,QFeatures-method", "version<-" ] }, { "page": "Parent", "title": "Parent name of a node", "topics": [ "Parent" ] }, { "page": "pepaTest", "title": "PEptide based Protein differential Abundance test", "topics": [ "pepaTest" ] }, { "page": "Pipelines", "title": "List of available pipelines in the package", "topics": [ "Pipelines" ] }, { "page": "pkgsRequire", "title": "Loads packages", "topics": [ "pkgsRequire" ] }, { "page": "compare-assays", "title": "Compare two assays", "topics": [ "plotCompareAssays" ] }, { "page": "plotJitter", "title": "Jitter plot of CC", "topics": [ "plotJitter" ] }, { "page": "plotJitter_rCharts", "title": "Display a a jitter plot for CC", "topics": [ "plotJitter_rCharts" ] }, { "page": "postHocTest", "title": "Post-hoc tests for classic 1-way ANOVA", "topics": [ "postHocTest" ] }, { "page": "pushpvalue", "title": "Push p-values based on metacell tags", "topics": [ "pushpvalue" ] }, { "page": "q_metacell", "title": "Quantitative metadata vocabulary for entities", "topics": [ "custom_metacell_colors", "metacellDef", "Metacell_generic", "metacombine", "q_metacell", "searchMetacellTags", "Set_POV_MEC_tags", "Set_POV_MEC_tags2", "UpdateMetacellAfterImputation", "UpdateMetacellAfterImputation,SummarizedExperiment-method" ] }, { "page": "QFeatures-excel", "title": "Exports a 'QFeatures' object to a Excel file.", "topics": [ "addColors", "QFeatures-excel", "write2excel", "write2excel,QFeatures-method", "write2excel,SummarizedExperiment-method", "write2excelSE" ] }, { "page": "QFeatures-filtering-oneSE", "title": "Filter features of one SE based on their rowData", "topics": [ "DaparToolsehd,", "filterFeaturesOneSE", "filterFeaturesOneSE,", "filterFeaturesOneSE,QFeatures-method", "FunctionFilter", "FunctionFilter,", "FunctionFilter-class", "QFeatures-filtering-oneSE", "VariableFilter" ] }, { "page": "QFeatures-utils", "title": "Utility funcitons to dela with QFeatures objects.", "topics": [ "last_assay", "n_assays_in_qf", "QFeatures-utils", "QFeaturesFromSE" ] }, { "page": "ReplaceSpecialChars", "title": "Standardize names", "topics": [ "ReplaceSpecialChars" ] }, { "page": "RunAggregation", "title": "Aggregation of peptide-level assay QFeatures", "topics": [ "RunAggregation" ] }, { "page": "samLRT", "title": "Computes a regularized version of the likelihood ratio statistic", "topics": [ "samLRT" ] }, { "page": "separateAdjPval", "title": "Computes the adjusted p-values separately on contrast using CP4P", "topics": [ "separateAdjPval" ] }, { "page": "SetHistory", "title": "Standardize names", "topics": [ "SetHistory" ] }, { "page": "splitAdjacencyMat", "title": "splits an adjacency matrix into specific and shared", "topics": [ "splitAdjacencyMat" ] }, { "page": "subR25pept", "title": "subR25pept dataset", "topics": [ "subR25pept" ] }, { "page": "subR25prot", "title": "subR25prot dataset", "topics": [ "subR25prot" ] }, { "page": "qMetacell-filter", "title": "Search lines which respects request on one or more conditions.", "topics": [ "qMetacell-filter", "qMetacellFilteringScope", "qMetacellOnConditions", "qMetacellWholeLine", "qMetacellWholeMatrix", "SymFilteringOperators" ] }, { "page": "testAnovaModels", "title": "Applies a statistical test on each element of a list of linear models", "topics": [ "testAnovaModels" ] }, { "page": "testDesign", "title": "Check the validity of the design", "topics": [ "testDesign" ] }, { "page": "thresholdpval4fdr", "title": "Applies p-value adjustment using cp4p on p-values below a given threshold", "topics": [ "thresholdpval4fdr" ] }, { "page": "translatedRandomBeta", "title": "Generator of simulated values", "topics": [ "translatedRandomBeta" ] }, { "page": "wrapperCalibrationPlot", "title": "Performs a calibration plot on an 'SummarizedExperiment' object, calling the 'cp4p' package functions.", "topics": [ "wrapperCalibrationPlot" ] }, { "page": "wrapperClassic1wayAnova", "title": "Wrapper for One-way Anova statistical test", "topics": [ "wrapperClassic1wayAnova" ] }, { "page": "wrapperDaparImputeMI", "title": "Missing values imputation using the LSimpute algorithm.", "topics": [ "wrapperDaparImputeMI" ] }, { "page": "wrapperImputeMLE", "title": "Imputation of peptides having no values in a biological condition.", "topics": [ "wrapperImputeMLE" ] }, { "page": "wrapperImputePA2", "title": "Missing values imputation from a 'SummarizedExperiment' object", "topics": [ "wrapperImputePA2" ] }, { "page": "wrapperPirat", "title": "Missing values imputation using Pirat", "topics": [ "wrapperPirat" ] } ], "_readme": "https://github.com/bioc/DaparToolshed/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationFilter", "askpass", "backports", "base64enc", "Biobase", "BiocBaseUtils", "BiocGenerics", "bit", "bit64", "boot", "broom", "bslib", "cachem", "car", "carData", "cli", "clipr", "clue", "cluster", "codetools", "colorspace", "cowplot", "cp4p", "cpp11", "crayon", "crosstalk", "curl", "data.table", "DelayedArray", "Deriv", "digest", "doBy", "doParallel", "dplyr", "DT", "ellipse", "emmeans", "estimability", "evaluate", "FactoMineR", "farver", "fastmap", "flashClust", "FNN", "fontawesome", "fontBitstreamVera", "fontLiberation", "fontquiver", "forcats", "foreach", "forecast", "Formula", "fracdiff", "fs", "gdtools", "geeM", "geepack", "generics", "GenomicRanges", "ggformula", "ggiraph", "ggplot2", "ggrepel", "ggridges", "glmnet", "glue", "graph", "gtable", 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