# A package for the clinical proteomic profiling data analysis

## Documentation for package ‘clippda’ version 1.40.0

- 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