Package: clippda 1.57.0

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

Peer review:

Datasets:
  • liverRawData - A dataframe of the protein expression data, peak information and sample information
  • liver_pheno - A dataframe of phenotypic information
  • liverdata - A dataframe of the protein expression data, peak information, and sample information
  • pheno_urine - A dataframe of phenotypic information

On BioConductor:clippda-1.55.0(bioc 3.20)clippda-1.54.0(bioc 3.19)

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

proteomicsonechannelpreprocessingdifferentialexpressionmultiplecomparison

3.30 score 2 scripts 252 downloads 22 exports 35 dependencies

Last updated 23 days agofrom:d7fcfbb26f. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 30 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 30 2024
R-4.4-macNOTEOct 30 2024
R-4.3-winNOTEOct 30 2024
R-4.3-macNOTEOct 30 2024

Exports:betweensampleVariancecheckNo.replicatesffisherInformationmostSimilarTwonegativeIntensitiesCorrectionphenoDataFramepreProcRepeatedPeakDataproteomicsExprsDataproteomicspDatareplicateCorrelationssample_technicalVariancesampleClusteredDatasampleSizesampleSize3DscatterPlotssampleSizeContourPlotssampleSizeParametersshowspectrumFilterztwoZvaluescasesVcontrolsPlotsZvaluesfrommultinomPlots

Dependencies:base64encBiobaseBiocGenericsbslibcachemclidigestevaluatefastmapfontawesomefsgluehighrhtmltoolshtmlwidgetsjquerylibjsonliteknitrlatticelifecyclelimmamagrittrmemoisemimeR6rappdirsrglrlangrmarkdownsassscatterplot3dstatmodtinytexxfunyaml

Sample Size Calculation

Rendered fromclippda.Rnwusingutils::Sweaveon Oct 30 2024.

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

Readme and manuals

Help Manual

Help pageTopics
A package for clinical proteomics profiling data analysisclippda-package clippda
Class "aclinicalProteomicsData"aclinicalProteomicsData aclinicalProteomicsData-class
S4 method for the aclinicalProteomicsData classaclinicalProteomicsData-methods
A generic function for computing the biological variance and mean differences between cases and controlsbetweensampleVariance biologicalVariance
Methods for Function betweensampleVariancebetweensampleVariance,aclinicalProteomicsData-method betweensampleVariance-methods
A function to detect disparity in the number of replicates across assayscheckNo.replicates
A function to compute adjustments for the effct of covariates (Z values) for an experiment with a binary exposure and a binary confounderf
A generic function to compute the heterogeneity correction factor in sample size calculationsfisherInformation
Methods for Function fisherInformationfisherInformation,aclinicalProteomicsData-method fisherInformation-methods
A dataframe of phenotypic informationliver_pheno
A dataframe of the protein expression data, peak information, and sample informationliverdata
A dataframe of the protein expression data, peak information and sample informationliverRawData
A function which indentifies two columns of a matrix, or dataframe, with the highest pairwise positive correlationsmostSimilarTwo
A function to correct the data for the negative intensities caused by the normalization and background correction procedures of mass spectrometry datanegativeIntensitiesCorrection
A dataframe of phenotypic informationpheno_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 datapreProcRepeatedPeakData
A generic fuction to extract duplicate SELDI data from an object of aclinicalProteomicsData class in the same format as the data from Biomarkers wizardproteomicsExprsData
Methods for Function proteomicsExprsDataproteomicsExprsData,aclinicalProteomicsData-method proteomicsExprsData-methods
A function to extract a dataframe of phenotypic information from an object of aclinicalProteomicsData classproteomicspData
Methods for Function proteomicspDataproteomicspData,aclinicalProteomicsData-method proteomicspData-methods
A generic function to compute intraclass correlationsintraclassCorrelations replicateCorrelations
Methods for Function replicateCorrelationsreplicateCorrelations,aclinicalProteomicsData-method replicateCorrelations-methods
A generic function for computing the technical variancesample_technicalVariance withinsampleVariance
Methods for Function sample_technicalVariancesample_technicalVariance,aclinicalProteomicsData-method sample_technicalVariance-methods
A function to arrange the data in sample-wise pairssampleClusteredData
A function for sample size calculationssampleSize
~~ Methods for Function sampleSizesampleSize,aclinicalProteomicsData,numeric,numeric-method sampleSize-methods
A function for 3D display of sample size in a multi parameter spacesampleSize3DscatterPlots
A function to construct a grid with contours for calculating sample size in multi dimensional parameter spacesampleSizeContourPlots
A generic function to calculate sample size parameterssampleSizeParameters
~~ Methods for Function sampleSizeParameterssampleSizeParameters,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 informationspectrumFilter
A function to compute Z values when there are no covariates other than the cancer classztwo
A function for ploting the odds of being a case vs control and their effects on adjustments for confoundersZvaluescasesVcontrolsPlots
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 valuesZvaluesfrommultinomPlots