Package: clippda 1.63.0

Stephen Nyangoma

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.

Authors:Stephen Nyangoma

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
clippda/json (API)

# Install 'clippda' in R:

install.packages('clippda', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

liver_pheno - A dataframe of phenotypic information
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
pheno_urine - A dataframe of phenotypic information

On BioConductor:clippda-1.63.0(bioc 3.24)clippda-1.62.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

proteomics onechannel preprocessing differentialexpression multiplecomparison

3.30 score 2 scripts 1 mentions 22 exports 35 dependencies

Last updated from:4bbcccb83f. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	186
linux-devel-x86_64	NOTE	257
source / vignettes	OK	243
linux-release-x86_64	NOTE	267
macos-release-arm64	NOTE	189
macos-oldrel-arm64	NOTE	214
windows-devel	NOTE	189
windows-release	NOTE	176
windows-oldrel	NOTE	162
wasm-release	OK	139

Exports:betweensampleVariance checkNo.replicates f fisherInformation mostSimilarTwo negativeIntensitiesCorrection phenoDataFrame preProcRepeatedPeakData proteomicsExprsData proteomicspData replicateCorrelations sample_technicalVariance sampleClusteredData sampleSize sampleSize3DscatterPlots sampleSizeContourPlots sampleSizeParameters show spectrumFilter ztwo ZvaluescasesVcontrolsPlots ZvaluesfrommultinomPlots

Dependencies:base64enc Biobase BiocGenerics bslib cachem cli digest evaluate fastmap fontawesome fs generics highr htmltools htmlwidgets jquerylib jsonlite knitr lattice lifecycle limma magrittr memoise mime R6 rappdirs rgl rlang rmarkdown sass scatterplot3d statmod tinytex xfun yaml

Sample Size Calculation

Rendered fromclippda.Rnwusingutils::Sweave

Last update: 2013-11-01
Started: 2013-11-01

Help page	Topics
A package for clinical proteomics profiling data analysis	clippda-package clippda
Class "aclinicalProteomicsData"	aclinicalProteomicsData aclinicalProteomicsData-class
S4 method for the aclinicalProteomicsData class	aclinicalProteomicsData-methods
A generic function for computing the biological variance and mean differences between cases and controls	betweensampleVariance biologicalVariance
Methods for Function betweensampleVariance	betweensampleVariance,aclinicalProteomicsData-method betweensampleVariance-methods
A function to detect disparity in the number of replicates across assays	checkNo.replicates
A function to compute adjustments for the effct of covariates (Z values) for an experiment with a binary exposure and a binary confounder	f
A generic function to compute the heterogeneity correction factor in sample size calculations	fisherInformation
Methods for Function fisherInformation	fisherInformation,aclinicalProteomicsData-method fisherInformation-methods
A dataframe of phenotypic information	liver_pheno
A dataframe of the protein expression data, peak information, and sample information	liverdata
A dataframe of the protein expression data, peak information and sample information	liverRawData
A function which indentifies two columns of a matrix, or dataframe, with the highest pairwise positive correlations	mostSimilarTwo
A function to correct the data for the negative intensities caused by the normalization and background correction procedures of mass spectrometry data	negativeIntensitiesCorrection
A dataframe of phenotypic information	pheno_urine
A generic function to set classes for the variables in the dataframe of phenotypic information.	phenoDataFrame
A function to pre-process repeated raw peak data	preProcRepeatedPeakData
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
Methods for Function proteomicsExprsData	proteomicsExprsData,aclinicalProteomicsData-method proteomicsExprsData-methods
A function to extract a dataframe of phenotypic information from an object of aclinicalProteomicsData class	proteomicspData
Methods for Function proteomicspData	proteomicspData,aclinicalProteomicsData-method proteomicspData-methods
A generic function to compute intraclass correlations	intraclassCorrelations replicateCorrelations
Methods for Function replicateCorrelations	replicateCorrelations,aclinicalProteomicsData-method replicateCorrelations-methods
A generic function for computing the technical variance	sample_technicalVariance withinsampleVariance
Methods for Function sample_technicalVariance	sample_technicalVariance,aclinicalProteomicsData-method sample_technicalVariance-methods
A function to arrange the data in sample-wise pairs	sampleClusteredData
A function for sample size calculations	sampleSize
~~ Methods for Function sampleSize	sampleSize,aclinicalProteomicsData,numeric,numeric-method sampleSize-methods
A function for 3D display of sample size in a multi parameter space	sampleSize3DscatterPlots
A function to construct a grid with contours for calculating sample size in multi dimensional parameter space	sampleSizeContourPlots
A generic function to calculate sample size parameters	sampleSizeParameters
~~ Methods for Function sampleSizeParameters	sampleSizeParameters,aclinicalProteomicsData,numeric,numeric-method sampleSizeParameters-methods
Methods for Function show in Package `methods'	show,aclinicalProteomicsData-method
A function to filter out samples with conflicting pair-wise compound information	spectrumFilter
A function to compute Z values when there are no covariates other than the cancer class	ztwo
A function for ploting the odds of being a case vs control and their effects on adjustments for confounders	ZvaluescasesVcontrolsPlots
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	ZvaluesfrommultinomPlots

Package: clippda 1.63.0

clippda: A package for the clinical proteomic profiling data analysis

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