clippda-package |
A package for clinical proteomics profiling data analysis |
aclinicalProteomicsData-class |
Class "aclinicalProteomicsData" |
aclinicalProteomicsData-methods |
S4 method for the aclinicalProteomicsData class |
betweensampleVariance |
A generic function for computing the biological variance and mean differences
between cases and controls |
betweensampleVariance,aclinicalProteomicsData |
A generic function for computing the biological variance and mean differences
between cases and controls |
betweensampleVariance,aclinicalProteomicsData-method |
Methods for Function betweensampleVariance |
betweensampleVariance-methods |
Methods for Function betweensampleVariance |
biologicalVariance |
A generic function for computing the biological variance and mean differences
between cases and controls |
checkNo.replicates |
A function to detect disparity in the number of replicates across assays |
clippda |
A package for clinical proteomics profiling data analysis |
fisherInformation |
A generic function to compute the heterogeneity correction factor in sample
size calculations |
fisherInformation,aclinicalProteomicsData-method |
Methods for Function fisherInformation |
fisherInformation-methods |
Methods for Function fisherInformation |
intraclassCorrelations |
A generic function to compute intraclass correlations |
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 |
liver_pheno |
A dataframe of phenotypic information |
mostSimilarTwo |
A function which indentifies two columns of a matrix, or dataframe,
with the highest pairwise positive correlations |
negativeIntensitiesCorrection |
A function to correct the data for the negative
intensities caused by the normalization and background correction
procedures of mass spectrometry data |
phenoDataFrame |
A generic function to set classes for the variables in the dataframe of phenotypic information. |
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
object of aclinicalProteomicsData class
in the same format as the data from
Biomarkers wizard |
proteomicsExprsData,aclinicalProteomicsData-method |
Methods for Function proteomicsExprsData |
proteomicsExprsData-methods |
Methods for Function proteomicsExprsData |
proteomicspData |
A function to extract a dataframe of phenotypic information from an
object of aclinicalProteomicsData class |
proteomicspData,aclinicalProteomicsData-method |
Methods for Function proteomicspData |
proteomicspData-methods |
Methods for Function proteomicspData |
replicateCorrelations |
A generic function to compute intraclass correlations |
replicateCorrelations,aclinicalProteomicsData-method |
Methods for Function replicateCorrelations |
replicateCorrelations-methods |
Methods for Function replicateCorrelations |
sampleClusteredData |
A function to arrange the data in sample-wise pairs |
sampleSize |
A function for sample size calculations |
sampleSize,aclinicalProteomicsData,numeric,numeric-method |
~~ Methods for Function sampleSize |
sampleSize-methods |
~~ Methods for Function sampleSize |
sampleSize3DscatterPlots |
A function for 3D display of sample size in a multi parameter space |
sampleSizeContourPlots |
A function to construct a grid with contours for calculating sample size in multi dimensional
parameter space |
sampleSizeParameters |
A generic function to calculate sample size parameters |
sampleSizeParameters,aclinicalProteomicsData,numeric,numeric-method |
~~ Methods for Function sampleSizeParameters |
sampleSizeParameters-methods |
~~ Methods for Function sampleSizeParameters |
sample_technicalVariance |
A generic function for computing the technical variance |
sample_technicalVariance,aclinicalProteomicsData-method |
Methods for Function sample_technicalVariance |
sample_technicalVariance-methods |
Methods for Function sample_technicalVariance |
show,aclinicalProteomicsData-method |
~~ Methods for Function show in Package 'methods' ~~ |
show,AnnotatedDataFrame-method |
~~ Methods for Function show in Package 'methods' ~~ |
show,ANY-method |
~~ Methods for Function show in Package 'methods' ~~ |
show,classRepresentation-method |
~~ Methods for Function show in Package 'methods' ~~ |
show,container-method |
~~ Methods for Function show in Package 'methods' ~~ |
show,eSet-method |
~~ Methods for Function show in Package 'methods' ~~ |
show,genericFunction-method |
~~ Methods for Function show in Package 'methods' ~~ |
show,MethodDefinition-method |
~~ Methods for Function show in Package 'methods' ~~ |
show,MethodSelectionReport-method |
~~ Methods for Function show in Package 'methods' ~~ |
show,MethodWithNext-method |
~~ Methods for Function show in Package 'methods' ~~ |
show,MIAME-method |
~~ Methods for Function show in Package 'methods' ~~ |
show,ObjectsWithPackage-method |
~~ Methods for Function show in Package 'methods' ~~ |
show,oldClass-method |
~~ Methods for Function show in Package 'methods' ~~ |
show,ScalarCharacter-method |
~~ Methods for Function show in Package 'methods' ~~ |
show,ScalarObject-method |
~~ Methods for Function show in Package 'methods' ~~ |
show,signature-method |
~~ Methods for Function show in Package 'methods' ~~ |
show,traceable-method |
~~ Methods for Function show in Package 'methods' ~~ |
show,Versioned-method |
~~ Methods for Function show in Package 'methods' ~~ |
show,Versions-method |
~~ Methods for Function show in Package 'methods' ~~ |
show,VersionsNull-method |
~~ Methods for Function show in Package 'methods' ~~ |
show-methods |
~~ Methods for Function show in Package 'methods' ~~ |
spectrumFilter |
A function to filter out samples with conflicting pair-wise compound
information |
withinsampleVariance |
A generic function for computing the technical variance |