| analyzeNormalizations | Calculate measures for normalization results |
| calculateANOVAPValues | Calculates ANOVA p-values comparing the different condition... |
| calculateAvgMadMem | Calculate average MAD (Median Absolute Deviation) for each... |
| calculateAvgReplicateVariation | Calculate average variance for each feature in each condition... |
| calculateContrasts | Performs statistical comparisons between the supplied... |
| calculateCorrSum | Calculates internal correlations for each condition having at... |
| calculateFeatureCV | Calculate CV values for each feature. Iterates through each... |
| calculatePercentageAvgDiffInMat | General function for calculating percentage difference of... |
| calculateReplicateCV | Calculate CV per replicate group and normalization technique |
| calculateSummarizedCorrelationVector | Calculates correlation values between replicates for each... |
| createDirectory | Create directory, or return error if already present |
| detectSingleReplicate | Detect single replicate, and assign related logical |
| detectSingletonSample | Detect single sample group |
| elapsedSecondsBetweenSystimes | Get number of seconds between two Sys.time() objects |
| example_data | Small example dataset used to demonstrate code consistency in... |
| example_data_only_values | Same data as in "example_data", but omitting the annotation... |
| example_design | Design matrix corresponding to the small example datasets. |
| example_stat_data | Same data as in "example_data", but normalized and ready for... |
| example_stat_summarized_experiment | SummarizedExperiment object prepared with design-matrix,... |
| example_summarized_experiment | SummarizedExperiment object prepared with design-matrix,... |
| example_wide_data | Full raw NormalyzerDE matrix used for internal testing |
| example_wide_design | Design matrix belonging together with example_wide_data. Used... |
| filterLowRep | Filter rows with lower than given number of replicates for... |
| findLowlyVariableFeaturesCVs | Uses a list of FDR-values to extract features with low... |
| generateAnnotatedMatrix | Generate an annotated data frame from statistics object |
| generatePlots | Generates a number of visualizations for the performance... |
| generateStatsReport | Generate full output report plot document. Plots p-value... |
| getCombinedMatrix | Merge multiple dataframes using provided function |
| getIndexList | Return list containing vector positions of values in string |
| getLowCountSampleFiltered | Verify that samples contain at least a lowest number of... |
| getReplicateSortedData | Get dataframe with raw data column sorted on replicates |
| getRowNAFilterContrast | Get contrast vector (TRUE/FALSE-values) indicating whether... |
| getRTNormalizedMatrix | Perform RT-segmented normalization by performing the supplied... |
| getSmoothedRTNormalizedMatrix | Generate multiple RT time-window normalized matrices where... |
| getVerifiedNormalyzerObject | Verify that input data is in correct format, and if so,... |
| getWidenedRTRange | Pick datapoints before and after window until a minimum... |
| globalIntensityNormalization | The normalization divides the intensity of each variable in a... |
| loadData | Load raw data into dataframe |
| loadDesign | Load raw design into dataframe |
| loadRawDataFromFile | Try reading raw Normalyzer matrix from provided filepath |
| meanNormalization | Intensity of each variable in a given sample is divided by... |
| medianNormalization | Intensity of each variable in a given sample is divided by... |
| normalyzer | NormalyzerDE pipeline entry point |
| NormalyzerDataset | Represents raw input data together with basic annotation... |
| normalyzerDE | NormalyzerDE differential expression |
| NormalyzerEvaluationResults | Representation of evaluation results by calculating... |
| NormalyzerResults | Representation of the results from performing normalization... |
| NormalyzerStatistics | Class representing a dataset for statistical processing in... |
| normMethods | Perform normalizations on Normalyzer dataset |
| performCyclicLoessNormalization | Cyclic Loess normalization |
| performGlobalRLRNormalization | Global linear regression normalization |
| performNoNormalization | Do no normalization (For debugging purposes) |
| performNormalizations | Main function for executing normalizations |
| performQuantileNormalization | Quantile normalization is performed by the function... |
| performSMADNormalization | Median absolute deviation normalization Normalization... |
| performVSNNormalization | Log2 transformed data is normalized using the function... |
| plotBoxPlot | Boxplots showing distribution of values after different... |
| plotComparisonVenns | If multiple comparisons - Show overlap in Venn diagrams |
| plotContrastPCA | Show in a PCA plot what samples are compared in statistical... |
| plotContrastPHists | Takes an NormalyzerStatistics instance and generates and... |
| plotCorrelation | Visualize within-replicates correlations |
| plotCVvsIntensity | Plots page displaying coefficient of variance (CV) against... |
| plotDendrograms | Visualize dendrogram grouping of samples |
| plotDensity | Density plots showing value distributions after... |
| plotFrontPage | Generate first page in output report and write to viewport |
| plotMA | Produces a page containing expression vs. fold-change figures... |
| plotMDS | MDS plots showing grouping of samples after normalizations |
| plotMeanSD | Visualize standard deviation over (expression?) for different... |
| plotPHist | Generate P-histograms for ANOVA calculated after each... |
| plotQQ | Produces page showing QQ-plots for the first sample for each... |
| plotReplicateVarAndStableVariables | Write figures displaying pooled coefficient of variance,... |
| plotReplicateVariance | Generate normalization replicate variance summary by... |
| plotRLE | Boxplots showing relative log expression after normalizations |
| plotSampleMappingPage | Write page with sample mapping |
| plotSampleOutlierSummary | Write page containing sample summary of intensities, missing... |
| plotScatter | Produces page containing scatter plot plotting the first two... |
| plotSigScatter | Takes an NormalyzerStatistics instance and generates and... |
| preprocessData | Replace empty values (0 or empty field) with NA in input data |
| printMeta | Print meta information for Normalyzer plot page ! Needs... |
| printPlots | Generate PDF grid page filling it with provided list of plots |
| reduceTechnicalReplicates | Remove technical replicates from data and design |
| setupJobDir | Create empty directory for run |
| setupPlotting | Setup PDF report settings by initializing the color palette,... |
| setupRawContrastObject | Prepare SummarizedExperiment object for statistics data |
| setupRawDataObject | Prepare SummarizedExperiment object for raw data to be... |
| setupTestData | Generate a random test dataset with features, sample values... |
| validateSampleReplication | Check whether all samples have replicates |
| verifyContrasts | Check that a given contrast string is valid given a... |
| verifyDesignMatrix | Verify that design matrix setup matches the data matrix |
| verifyMultipleSamplesPresent | Check whether more than one sample is present |
| verifySummarizedExperiment | Verify that design matrix setup matches the data matrix |
| verifyValidNumbers | Verify that input fields conform to the expected formats |
| writeNormalizedDatasets | Write normalization matrices to file |
