A package for the clinical proteomic profiling data analysis


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Documentation for package ‘clippda’ version 1.30.0

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clippda-package A package for clinical proteomics profiling data analysis
aclinicalProteomicsData Class "aclinicalProteomicsData"
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-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
f A function to compute adjustments for the effct of covariates (Z values) for an experiment with a binary exposure and a binary confounder
fisherInformation A generic function to compute the heterogeneity correction factor in sample size calculations
fisherInformation-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-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-method Methods for Function proteomicspData
proteomicspData-methods Methods for Function proteomicspData
replicateCorrelations A generic function to compute intraclass correlations
replicateCorrelations-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-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-method ~~ Methods for Function sampleSizeParameters
sampleSizeParameters-methods ~~ Methods for Function sampleSizeParameters
sample_technicalVariance A generic function for computing the technical variance
sample_technicalVariance-method Methods for Function sample_technicalVariance
sample_technicalVariance-methods Methods for Function sample_technicalVariance
show-method 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
ztwo A function to compute Z values when there are no covariates other than the cancer class
ZvaluescasesVcontrolsPlots A function for ploting the odds of being a case vs control and their effects on adjustments for confounders
ZvaluesfrommultinomPlots A generic functon to plot Density of Z values from a simulation from a multinomial population using the balanced and unbalanced studies and a 3D representaion of the Z values