clippda: A package for the clinical proteomic profiling data analysis
Version 1.26.0

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
Bioconductor views DifferentialExpression MultipleComparison OneChannel Preprocessing Proteomics
Date of publicationNone
MaintainerStephen Nyangoma <s.o.nyangoma@bham.ac.uk>
LicenseGPL (>=2)
Version1.26.0
URL http://www.cancerstudies.bham.ac.uk/crctu/CLIPPDA.shtml
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("clippda")

Getting started

Package overview

Popular man pages

clippda-package: A package for clinical proteomics profiling data analysis
f: A function to compute adjustments for the effct of covariates...
liverdata: A dataframe of the protein expression data, peak information,...
proteomicspData-methods: Methods for Function proteomicspData
sampleClusteredData: A function to arrange the data in sample-wise pairs
ztwo: A function to compute Z values when there are no covariates...
ZvaluescasesVcontrolsPlots: A function for ploting the odds of being a case vs control...
See all...

All man pages Function index File listing

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
f: A function to compute adjustments for the effct of covariates...
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...
ztwo: A function to compute Z values when there are no covariates...
ZvaluescasesVcontrolsPlots: A function for ploting the odds of being a case vs control...
ZvaluesfrommultinomPlots: A generic functon to plot Density of Z values from a...

Functions

Files

DESCRIPTION
NAMESPACE
R
R/ZvaluescasesVcontrolsPlots.R
R/ZvaluesfrommultinomPlots.R
R/aclinicalProteomicData.class.R
R/aclinicalProteomicData.methods.R
R/betweensampleVariance.Generic.R
R/betweensampleVariance.Method.R
R/checkNo.replicates.R
R/f.R
R/fisherInformation.Generic.R
R/fisherInformation.Method.R
R/mostSimilarTwo.R
R/negativeIntensitiesCorrection.R
R/phenoDataFrame.R
R/preProcRepeatedPeakData.R
R/proteomicsExprsData.Generic.R
R/proteomicsExprsData.Method.R
R/proteomicspData.Generic.R
R/proteomicspData.Method.R
R/replicateCorrelations.Generic.R
R/replicateCorrelations.Method.R
R/sampleClusteredData.R
R/sampleSize3DscatterPlots.R
R/sampleSizeContourPlots.R
R/sampleSizeGeneric.R
R/sampleSizeMethod.R
R/sampleSizeParameters.Generic.R
R/sampleSizeParameters.Method.R
R/sample_technicalVaraiance.Generic.R
R/sample_technicalVariance.Method.R
R/spectrumFilter.R
R/ztwo.R
build
build/vignette.rds
data
data/liverRawData.rda
data/liver_pheno.rda
data/liverdata.rda
data/pheno_urine.rda
inst
inst/CITATION
inst/doc
inst/doc/clippda.R
inst/doc/clippda.Rnw
inst/doc/clippda.pdf
man
man/ZvaluescasesVcontrolsPlots.rd
man/ZvaluesfrommultinomPlots.Rd
man/aclinicalProteomicsData-class.Rd
man/aclinicalProteomicsData-methods.Rd
man/betweensampleVariance-methods.Rd
man/betweensampleVariance.Rd
man/checkNo.replicates.Rd
man/clippda-package.Rd
man/f.rd
man/fisherInformation-methods.Rd
man/fisherInformation.Rd
man/liverRawData.Rd
man/liver_pheno.Rd
man/liverdata.Rd
man/mostSimilarTwo.Rd
man/negativeIntensitiesCorrection.Rd
man/phenoDataFrame.Rd
man/pheno_urine.Rd
man/preProcRepeatedPeakData.Rd
man/proteomicsExprsData-methods.Rd
man/proteomicsExprsData.Rd
man/proteomicspData-methods.Rd
man/proteomicspData.Rd
man/replicateCorrelations-methods.Rd
man/replicateCorrelations.Rd
man/sampleClusteredData.Rd
man/sampleSize-methods.Rd
man/sampleSize.Rd
man/sampleSize3DscatterPlots.Rd
man/sampleSizeContourPlots.Rd
man/sampleSizeParameters-methods.Rd
man/sampleSizeParameters.Rd
man/sample_technicalVariance-methods.Rd
man/sample_technicalVariance.Rd
man/show-methods.Rd
man/spectrumFilter.Rd
man/ztwo.rd
vignettes
vignettes/LittBib.bib
vignettes/clippda.Rnw
clippda documentation built on May 20, 2017, 9:17 p.m.

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