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.

AuthorStephen Nyangoma
Date of publicationNone
MaintainerStephen Nyangoma <s.o.nyangoma@bham.ac.uk>
LicenseGPL (>=2)
Version1.24.0
http://www.cancerstudies.bham.ac.uk/crctu/CLIPPDA.shtml

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...

Functions

aclinicalProteomicsData Man page
aclinicalProteomicsData-class Man page
aclinicalProteomicsData-methods Man page
betweensampleVariance Man page
betweensampleVariance,aclinicalProteomicsData-method Man page
betweensampleVariance-methods Man page
biologicalVariance Man page
checkNo.replicates Man page
clippda Man page
clippda-package Man page
fisherInformation Man page
fisherInformation,aclinicalProteomicsData-method Man page
fisherInformation-methods Man page
intraclassCorrelations Man page
liverdata Man page
liver_pheno Man page
liverRawData Man page
mostSimilarTwo Man page
negativeIntensitiesCorrection Man page
phenoDataFrame Man page
pheno_urine Man page
preProcRepeatedPeakData Man page
proteomicsExprsData Man page
proteomicsExprsData,aclinicalProteomicsData-method Man page
proteomicsExprsData-methods Man page
proteomicspData Man page
proteomicspData,aclinicalProteomicsData-method Man page
proteomicspData-methods Man page
replicateCorrelations Man page
replicateCorrelations,aclinicalProteomicsData-method Man page
replicateCorrelations-methods Man page
sampleClusteredData Man page
sampleSize Man page
sampleSize3DscatterPlots Man page
sampleSize,aclinicalProteomicsData,numeric,numeric-method Man page
sampleSizeContourPlots Man page
sampleSize-methods Man page
sampleSizeParameters Man page
sampleSizeParameters,aclinicalProteomicsData,numeric,numeric-met Man page
sampleSizeParameters-methods Man page
sample_technicalVariance Man page
sample_technicalVariance,aclinicalProteomicsData-method Man page
sample_technicalVariance-methods Man page
show,aclinicalProteomicsData-method Man page
spectrumFilter Man page
withinsampleVariance Man page
ZvaluesfrommultinomPlots Man page

Files

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

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