Evaluation of normalization methods and calculation of differential expression analysis statistics

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 |

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