clippda-package | A package for clinical proteomics profiling data analysis |
aclinicalProteomicsData | Class "aclinicalProteomicsData" |
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-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-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-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-method | Methods for Function proteomicspData |
proteomicspData-methods | Methods for Function proteomicspData |
replicateCorrelations | A generic function to compute intraclass correlations |
replicateCorrelations-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-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-method | ~~ Methods for Function sampleSizeParameters |
sampleSizeParameters-methods | ~~ Methods for Function sampleSizeParameters |
sample_technicalVariance | A generic function for computing the technical variance |
sample_technicalVariance-method | Methods for Function sample_technicalVariance |
sample_technicalVariance-methods | Methods for Function sample_technicalVariance |
show-method | Class "aclinicalProteomicsData" |
spectrumFilter | A function to filter out samples with conflicting pair-wise compound information |
withinsampleVariance | A generic function for computing the technical variance |