clippda: A package for the clinical proteomic profiling data analysis

Methods for the nalysis of data from clinical proteomic profiling studies. The focus is on the studies of human subjects, which are often observational case-control by design and have technical replicates. A method for sample size determination for planning these studies is proposed. It incorporates routines for adjusting for the expected heterogeneities and imbalances in the data and the within-sample replicate correlations.

Author
Stephen Nyangoma
Date of publication
None
Maintainer
Stephen Nyangoma <s.o.nyangoma@bham.ac.uk>
License
GPL (>=2)
Version
1.24.0
URLs

View on Bioconductor

Man pages

aclinicalProteomicsData-class
Class "aclinicalProteomicsData"
aclinicalProteomicsData-methods
S4 method for the aclinicalProteomicsData class
betweensampleVariance
A generic function for computing the biological variance and...
betweensampleVariance-methods
Methods for Function betweensampleVariance
checkNo.replicates
A function to detect disparity in the number of replicates...
clippda-package
A package for clinical proteomics profiling data analysis
fisherInformation
A generic function to compute the heterogeneity correction...
fisherInformation-methods
Methods for Function fisherInformation
liverdata
A dataframe of the protein expression data, peak information,...
liver_pheno
A dataframe of phenotypic information
liverRawData
A dataframe of the protein expression data, peak information...
mostSimilarTwo
A function which indentifies two columns of a matrix, or...
negativeIntensitiesCorrection
A function to correct the data for the negative intensities...
phenoDataFrame
A generic function to set classes for the variables in the...
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...
proteomicsExprsData-methods
Methods for Function proteomicsExprsData
proteomicspData
A function to extract a dataframe of phenotypic information...
proteomicspData-methods
Methods for Function proteomicspData
replicateCorrelations
A generic function to compute intraclass correlations
replicateCorrelations-methods
Methods for Function replicateCorrelations
sampleClusteredData
A function to arrange the data in sample-wise pairs
sampleSize
A function for sample size calculations
sampleSize3DscatterPlots
A function for 3D display of sample size in a multi parameter...
sampleSizeContourPlots
A function to construct a grid with contours for calculating...
sampleSize-methods
~~ Methods for Function sampleSize
sampleSizeParameters
A generic function to calculate sample size parameters
sampleSizeParameters-methods
~~ Methods for Function sampleSizeParameters
sample_technicalVariance
A generic function for computing the technical variance
sample_technicalVariance-methods
Methods for Function sample_technicalVariance
show-methods
Methods for Function show in Package 'methods'
spectrumFilter
A function to filter out samples with conflicting pair-wise...
ZvaluesfrommultinomPlots
A generic functon to plot Density of Z values from a...

Files in this package

clippda/DESCRIPTION
clippda/NAMESPACE
clippda/R
clippda/R/ZvaluescasesVcontrolsPlots.R
clippda/R/ZvaluesfrommultinomPlots.R
clippda/R/aclinicalProteomicData.class.R
clippda/R/aclinicalProteomicData.methods.R
clippda/R/betweensampleVariance.Generic.R
clippda/R/betweensampleVariance.Method.R
clippda/R/checkNo.replicates.R
clippda/R/f.R
clippda/R/fisherInformation.Generic.R
clippda/R/fisherInformation.Method.R
clippda/R/mostSimilarTwo.R
clippda/R/negativeIntensitiesCorrection.R
clippda/R/phenoDataFrame.R
clippda/R/preProcRepeatedPeakData.R
clippda/R/proteomicsExprsData.Generic.R
clippda/R/proteomicsExprsData.Method.R
clippda/R/proteomicspData.Generic.R
clippda/R/proteomicspData.Method.R
clippda/R/replicateCorrelations.Generic.R
clippda/R/replicateCorrelations.Method.R
clippda/R/sampleClusteredData.R
clippda/R/sampleSize3DscatterPlots.R
clippda/R/sampleSizeContourPlots.R
clippda/R/sampleSizeGeneric.R
clippda/R/sampleSizeMethod.R
clippda/R/sampleSizeParameters.Generic.R
clippda/R/sampleSizeParameters.Method.R
clippda/R/sample_technicalVaraiance.Generic.R
clippda/R/sample_technicalVariance.Method.R
clippda/R/spectrumFilter.R
clippda/R/ztwo.R
clippda/build
clippda/build/vignette.rds
clippda/data
clippda/data/liverRawData.rda
clippda/data/liver_pheno.rda
clippda/data/liverdata.rda
clippda/data/pheno_urine.rda
clippda/inst
clippda/inst/CITATION
clippda/inst/doc
clippda/inst/doc/clippda.R
clippda/inst/doc/clippda.Rnw
clippda/inst/doc/clippda.pdf
clippda/man
clippda/man/ZvaluescasesVcontrolsPlots.rd
clippda/man/ZvaluesfrommultinomPlots.Rd
clippda/man/aclinicalProteomicsData-class.Rd
clippda/man/aclinicalProteomicsData-methods.Rd
clippda/man/betweensampleVariance-methods.Rd
clippda/man/betweensampleVariance.Rd
clippda/man/checkNo.replicates.Rd
clippda/man/clippda-package.Rd
clippda/man/f.rd
clippda/man/fisherInformation-methods.Rd
clippda/man/fisherInformation.Rd
clippda/man/liverRawData.Rd
clippda/man/liver_pheno.Rd
clippda/man/liverdata.Rd
clippda/man/mostSimilarTwo.Rd
clippda/man/negativeIntensitiesCorrection.Rd
clippda/man/phenoDataFrame.Rd
clippda/man/pheno_urine.Rd
clippda/man/preProcRepeatedPeakData.Rd
clippda/man/proteomicsExprsData-methods.Rd
clippda/man/proteomicsExprsData.Rd
clippda/man/proteomicspData-methods.Rd
clippda/man/proteomicspData.Rd
clippda/man/replicateCorrelations-methods.Rd
clippda/man/replicateCorrelations.Rd
clippda/man/sampleClusteredData.Rd
clippda/man/sampleSize-methods.Rd
clippda/man/sampleSize.Rd
clippda/man/sampleSize3DscatterPlots.Rd
clippda/man/sampleSizeContourPlots.Rd
clippda/man/sampleSizeParameters-methods.Rd
clippda/man/sampleSizeParameters.Rd
clippda/man/sample_technicalVariance-methods.Rd
clippda/man/sample_technicalVariance.Rd
clippda/man/show-methods.Rd
clippda/man/spectrumFilter.Rd
clippda/man/ztwo.rd
clippda/vignettes
clippda/vignettes/LittBib.bib
clippda/vignettes/clippda.Rnw