A package for the clinical proteomic profiling data analysis

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Documentation for package ‘clippda’ version 1.59.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

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