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DAPAR (version 1.4.7)
Tools for the Differential Analysis of Proteins Abundance with R
Description
This package contains a collection of functions for the visualisation and the statistical analysis of proteomic data.
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Version
Version
1.4.7
1.4.2
1.0.0
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Version
1.4.7
License
Artistic-2.0
Maintainer
Samuel Wieczorek
Last Published
June 27th, 2016
Functions in DAPAR (1.4.7)
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diffAnaGetSignificant
Returns a MSnSet object with only proteins significant after differential analysis.
diffAnaLimma
Performs differential analysis on an MSnSet object, calling the
limma
package functions
getPaletteForReplicates
Palette for plot the replicates in DAPAR
getPourcentageOfMV
Percentage of missing values
MeanPeptides
Compute the intensity of proteins as the mean of the intensities of their peptides.
MeanPeptidesSpeedUp
Compute the intensity of proteins as the mean of the intensities of their peptides.
pepAgregate
Function agregate peptides to proteins
pepAgregateSpeedUp
Function agregate peptides to proteins
wrapper.corrMatrixD
Displays a correlation matrix of the quantitative data of the
exprs()
table
wrapper.densityPlotD
Builds a densityplot from an object of class
MSnSet
wrapper.mvImage
Heatmap of missing values from a
MSnSet
object
wrapper.mvImputation
Missing values imputation from a
MSnSet
object
boxPlotD
Builds a boxplot from a dataframe
BuildAdjacencyMatrix
Function matrix of appartenance group
diffAna
This function performs a differential analysis on an MSnSet object (adapted from
limma
)
diffAnaComputeFDR
Computes the FDR corresponding to the p-values of the differential analysis using
CountPep
Compute the number of peptides used to aggregate proteins
createMSnset
Creates an object of class
MSnSet
from text file
diffAnaSave
Returns a
MSnSet
object with the results of the differential analysis performed with
limma
package.
diffAnaVolcanoplot
Volcanoplot of the differential analysis
getProcessingInfo
Returns the contains of the slot processing of an object of class MSnSet
getProteinsStats
computes the number of proteins that are only defined by specific peptides, shared peptides or a mixture of two.
testWithoutNA
Test dataset
test
Test dataset
UPSpep25
UPSpep25 dataset
varianceDistD
Distribution of variance of proteins
wrapper.mvPerLinesHistoPerCondition
Bar plot of missing values per lines and per conditions from an object
MSnSet
wrapper.mvPerLinesHisto
Histogram of missing values per lines from an object
MSnSet
mvImage
Heatmap of missing values
getPaletteForLabels
Palette for plots in DAPAR
getNumberOfEmptyLines
Returns the number of empty lines in the data
mvTypePlot
Distribution of missing values with respect to intensity values
normalizeD
Normalisation
mvImputation
Missing values imputation from a matrix
wrapper.diffAnaLimma
Performs differential analysis on an MSnSet object, calling the
limma
package functions
wrapper.mvTypePlot
Distribution of missing values with respect to intensity values from a
MSnSet
object
wrapper.diffAnaWelch
Performs a differential analysis on a
MSnSet
object using the Welch t-test
wrapper.normalizeD
Normalisation
writeMSnsetToExcel
This function exports a
MSnSet
object to a Excel file.
BuildColumnToProteinDataset
creates a column for the protein dataset after agregation by using the previous peptide dataset.
BuildSparseAdjacencyMatrix
Function matrix of appartenance group
diffAnaWelch
Performs a differential analysis on a
MSnSet
object using the Welch t-test
getIndicesConditions
Gets the conditions indices.
mvFilterGetIndices
Filter lines in the matrix of intensities w.r.t. some criteria
mvHisto
Histogram of missing values
SumPeptides
Compute the intensity of proteins with the sum of the intensities of their peptides.
wrapperCalibrationPlot
Performs a calibration plot on an
MSnSet
object, calling the
cp4p
package functions.
SumPeptidesSpeedUp
Compute the intensity of proteins with the sum of the intensities of their peptides.
wrapper.varianceDistD
Distribution of variance of proteins
compareNormalizationD
Builds a plot from a dataframe
GraphPepProt
Function to create a histogram that shows the repartition of peptides w.r.t. the proteins
corrMatrixD
Displays a correlation matrix of the quantitative data of the
exprs()
table.
mvFilter
Filter lines in the matrix of intensities w.r.t. some criteria
heatmap.DAPAR
This function is inspired from the function
heatmap.2
that displays quantitative data in the
exprs()
table of an object of class
MSnSet
. For more information, please refer to the help of the heatmap.2 function.
mvFilterFromIndices
Filter lines in the matrix of intensities w.r.t. some criteria
proportionConRev
Barplot of proportion of contaminants and reverse
removeLines
Removes lines in the dataset based on a prefix string.
wrapper.boxPlotD
Wrapper to the boxplotD function on an object
MSnSet
wrapper.compareNormalizationD
Builds a plot from a dataframe
deleteLinesFromIndices
Delete the lines in the matrix of intensities and the metadata table given their indice.
densityPlotD
Builds a densityplot from a dataframe
getIndicesOfLinesToRemove
Get the indices of the lines to delete, based on a prefix string
getNumberOf
Number of lines with prefix
heatmapD
This function is a wrapper to
heatmap.2
that displays quantitative data in the
exprs()
table of an object of class
MSnSet
limmaCompleteTest
Computes a hierarchical differential analysis
mvPerLinesHisto
Bar plot of missing values per lines
mvPerLinesHistoPerCondition
Bar plot of missing values per lines and per condition
topMaxUsingPartialSortIndices
Function to return the indices of the n higher values in the vector
wrapper.heatmapD
This function is a wrapper to
heatmap.2
that displays quantitative data in the
exprs()
table of an object of class
MSnSet
TopnPeptides
Compute the intensity of proteins as the sum of the intensities of their n best peptides.
wrapper.mvHisto
Histogram of missing values from a
MSnSet
object