Learn R Programming

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.

Copy Link

Version

Version

1.4.7

License

Artistic-2.0

Maintainer

Samuel Wieczorek

Last Published

February 15th, 2017

Functions in DAPAR (1.4.7)

diffAnaGetSignificant

Returns a MSnSet object with only proteins significant after differential analysis.

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

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.

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

Builds a boxplot from a dataframe

BuildAdjacencyMatrix

Function matrix of appartenance group

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

Compute the number of peptides used to aggregate proteins

Creates an object of class MSnSet from text file

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.

UPSpep25 dataset

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

Heatmap of missing values

getPaletteForLabels

Palette for plots in DAPAR

getNumberOfEmptyLines

Returns the number of empty lines in the data

Distribution of missing values with respect to intensity values

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

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

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

Histogram of missing values

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

Function to create a histogram that shows the repartition of peptides w.r.t. the proteins

Displays a correlation matrix of the quantitative data of the exprs() table.

Filter lines in the matrix of intensities w.r.t. some criteria

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

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.

Builds a densityplot from a dataframe

getIndicesOfLinesToRemove

Get the indices of the lines to delete, based on a prefix string

Number of lines with prefix

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

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