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| clippda-package | A package for clinical proteomics profiling data analysis |
| aclinicalProteomicsData-class | Class "aclinicalProteomicsData" |
| aclinicalProteomicsData-methods | S4 method for the aclinicalProteomicsData class |
| betweensampleVariance | A generic function for computing the biological variance and mean differences between cases and controls |
| betweensampleVariance,aclinicalProteomicsData | A generic function for computing the biological variance and mean differences between cases and controls |
| betweensampleVariance,aclinicalProteomicsData-method | Methods for Function betweensampleVariance |
| betweensampleVariance-methods | Methods for Function betweensampleVariance |
| biologicalVariance | A generic function for computing the biological variance and mean differences between cases and controls |
| checkNo.replicates | A function to detect disparity in the number of replicates across assays |
| clippda | A package for clinical proteomics profiling data analysis |
| fisherInformation | A generic function to compute the heterogeneity correction factor in sample size calculations |
| fisherInformation,aclinicalProteomicsData-method | Methods for Function fisherInformation |
| fisherInformation-methods | Methods for Function fisherInformation |
| intraclassCorrelations | A generic function to compute intraclass correlations |
| liverdata | A dataframe of the protein expression data, peak information, and sample information |
| liverRawData | A dataframe of the protein expression data, peak information and sample information |
| liver_pheno | A dataframe of phenotypic information |
| mostSimilarTwo | A function which indentifies two columns of a matrix, or dataframe, with the highest pairwise positive correlations |
| negativeIntensitiesCorrection | A function to correct the data for the negative intensities caused by the normalization and background correction procedures of mass spectrometry data |
| phenoDataFrame | A generic function to set classes for the variables in the dataframe of phenotypic information. |
| pheno_urine | A dataframe of phenotypic information |
| preProcRepeatedPeakData | A function to pre-process repeated raw peak data |
| proteomicsExprsData | A generic fuction to extract duplicate SELDI data from an object of aclinicalProteomicsData class in the same format as the data from Biomarkers wizard |
| proteomicsExprsData,aclinicalProteomicsData-method | Methods for Function proteomicsExprsData |
| proteomicsExprsData-methods | Methods for Function proteomicsExprsData |
| proteomicspData | A function to extract a dataframe of phenotypic information from an object of aclinicalProteomicsData class |
| proteomicspData,aclinicalProteomicsData-method | Methods for Function proteomicspData |
| proteomicspData-methods | Methods for Function proteomicspData |
| replicateCorrelations | A generic function to compute intraclass correlations |
| replicateCorrelations,aclinicalProteomicsData-method | Methods for Function replicateCorrelations |
| replicateCorrelations-methods | Methods for Function replicateCorrelations |
| sampleClusteredData | A function to arrange the data in sample-wise pairs |
| sampleSize | A function for sample size calculations |
| sampleSize,aclinicalProteomicsData,numeric,numeric-method | ~~ Methods for Function sampleSize |
| sampleSize-methods | ~~ Methods for Function sampleSize |
| sampleSize3DscatterPlots | A function for 3D display of sample size in a multi parameter space |
| sampleSizeContourPlots | A function to construct a grid with contours for calculating sample size in multi dimensional parameter space |
| sampleSizeParameters | A generic function to calculate sample size parameters |
| sampleSizeParameters,aclinicalProteomicsData,numeric,numeric-method | ~~ Methods for Function sampleSizeParameters |
| sampleSizeParameters-methods | ~~ Methods for Function sampleSizeParameters |
| sample_technicalVariance | A generic function for computing the technical variance |
| sample_technicalVariance,aclinicalProteomicsData-method | Methods for Function sample_technicalVariance |
| sample_technicalVariance-methods | Methods for Function sample_technicalVariance |
| show,aclinicalProteomicsData-method | ~~ Methods for Function show in Package 'methods' ~~ |
| show,AnnotatedDataFrame-method | ~~ Methods for Function show in Package 'methods' ~~ |
| show,ANY-method | ~~ Methods for Function show in Package 'methods' ~~ |
| show,classRepresentation-method | ~~ Methods for Function show in Package 'methods' ~~ |
| show,container-method | ~~ Methods for Function show in Package 'methods' ~~ |
| show,eSet-method | ~~ Methods for Function show in Package 'methods' ~~ |
| show,genericFunction-method | ~~ Methods for Function show in Package 'methods' ~~ |
| show,MethodDefinition-method | ~~ Methods for Function show in Package 'methods' ~~ |
| show,MethodSelectionReport-method | ~~ Methods for Function show in Package 'methods' ~~ |
| show,MethodWithNext-method | ~~ Methods for Function show in Package 'methods' ~~ |
| show,MIAME-method | ~~ Methods for Function show in Package 'methods' ~~ |
| show,ObjectsWithPackage-method | ~~ Methods for Function show in Package 'methods' ~~ |
| show,oldClass-method | ~~ Methods for Function show in Package 'methods' ~~ |
| show,ScalarCharacter-method | ~~ Methods for Function show in Package 'methods' ~~ |
| show,ScalarObject-method | ~~ Methods for Function show in Package 'methods' ~~ |
| show,signature-method | ~~ Methods for Function show in Package 'methods' ~~ |
| show,traceable-method | ~~ Methods for Function show in Package 'methods' ~~ |
| show,Versioned-method | ~~ Methods for Function show in Package 'methods' ~~ |
| show,Versions-method | ~~ Methods for Function show in Package 'methods' ~~ |
| show,VersionsNull-method | ~~ Methods for Function show in Package 'methods' ~~ |
| show-methods | ~~ Methods for Function show in Package 'methods' ~~ |
| spectrumFilter | A function to filter out samples with conflicting pair-wise compound information |
| withinsampleVariance | A generic function for computing the technical variance |