A package for the clinical proteomic profiling data analysis


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Documentation for package ‘clippda’ version 1.0.0

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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