Man pages for elqumsan/RNAseqMVA
Application of Multivariate Analysis methods to RNA-seq Data
| buildAttributes | build attributes for an object depending on its class |
| buildAttributes.DataTableWithClasses | build the attributes of an object of class... |
| buildAttributes.DataTableWithTrainTestSets | build the attributes that depend on the count table |
| buildAttributes.default | default method to build attributes for an object. |
| DataTableWithClasses | constructor of the DataTableWithClasses class |
| DataTableWithTrainTestSets | Random sampling of n training sets in a DataTableWithClasses. |
| DEGordering | Variable ordering according to the p-values returned by... |
| ErrorRateBoxPlot | Function for boxplot the error rate |
| exportTables | Export the different fields of an object in tab-separated... |
| exportTables.DataTableWithClasses | Export the different fields of an object of class... |
| exportTables.DataTableWithTrainTestSets | Export the tables specific to the class... |
| exportTables.default | default export table (for closing the NextMethod calls) |
| exportTables.StudyCase | Export the tables specific to the class StudyCase |
| ExtractPhenoTable | Fuction for extracting Pheno Table from specified recount... |
| filterDataTable | Apply various filters on the observations and variables of a... |
| geocharFromPheno | Extract the conditions from the "characteristics" column of... |
| heatmap.TrainTestResult | heat map is a fales color image with pattern added to the... |
| histCountsPerGeneClass | Draw an histogram with the raw counts per gene |
| histCountsPerGeneClass.StudyCase | Draw an histogram with the raw counts per gene |
| initParallelComputing | initialise parameters for parallel computing with foreach and... |
| initRecountID | Intialise parameters and directories for a give recount ID. |
| IterateTrainingTesting | Iterate training/testing procedures with a given classifier... |
| LibsizeBarplot | Draw a barplot with the number of million reads per sample |
| LibsizeRankPlot | Rank plot of RNA-seq library sizes |
| loadCounts | Loading the count table, the Pheno table and vector of class... |
| loadMemoryImage | Load a previous analysis previously stored as memoy image |
| loadRecountExperiment | Loading one count table from Recount repository by given... |
| LoadRequiredBioconductorPackages | Load required packages from BioConductor, afte having... |
| LoadRequiredCRANPackages | Load required packages from CRAN, after having installed them... |
| MergeRuns | Merge read counts from different runs by sample. |
| message.with.time | print a message preceded by currrent time |
| MisclassificationEstimate | RNA-Seq classifier evaluation to assesse the performance of... |
| NormalizeSamples | scaling RNA-seq count table |
| outputParameters | Compute output parameters for an RNAseqMVA analysis |
| plot2PCs | Plot two components of prcomp transform |
| plotFigures | plot diagnostic figures for specific classes of objects |
| plotFigures.DataTableWithClasses | plot diagnostic figures for an object of the class... |
| plotFilterHistograms | plot histograms of the variance distributions at different... |
| plotKNNtuning | draw plots to highlight the results of KNN tuning |
| plotRFtuning | draw plots to highlight the results of ranfomForest tuning |
| plotSVMtuning | draw plots to highlight the results of SVM tuning |
| print.DataTableWithClasses | finish summary of an object belonging to class... |
| print.DataTableWithTrainTestSets | print of an object belonging to class... |
| print.StudyCase | print a summary of an object belonging to class StudyCase |
| print.TrainTestResult | printing the attribute of object that had TraiTestResult... |
| RunDESeq2 | run DESeq2 to test differential expression on each feature of... |
| RunDESeq2.StudyCase | run DESeq2 on an object of class StudyCase |
| RunedgeR | run edgeR to test differential expression on each feature of... |
| RunedgeR.StudyCase | run edgeR on an object of class StudyCase |
| RunViRf | run variable importance by random Forest to on an object of... |
| RunViRf.StudyCase | run variable importance by random Forest on an object of... |
| saveMemoryImage | Save a memory image in order to be able to reload all results... |
| selectProjectsByCharacteristics | Select Recount projects based on the presence of... |
| StratifiedSampling | stratified sampling |
| StudyCase | Create a StudyCase object, load RecountID dataset, and... |
| SummarizeErrorTable | generate a summary table from a list of error table files. |
| SummarizeTrainTestResults | Summarize results of several training-testing experiments. |
| summary.DataTableWithClasses | print a summary of an object belonging to class... |
| summary.DataTableWithTrainTestSets | print a summary of an object belonging to class... |
| summary.default | finish summary of an object belonging to class... |
| summary.StudyCase | print a summary of an object belonging to class StudyCase |
| TrainTestResult | Class to handle the results of Training-Testing evaluation... |
| TuneClassifiers | Tune the parameters of the different classifiers for a given... |
| XYplot | Draw an XY plot to compare the mean counts per gene for two... |
