Package 'Doscheda'

Title: A DownStream Chemo-Proteomics Analysis Pipeline
Description: Doscheda focuses on quantitative chemoproteomics used to determine protein interaction profiles of small molecules from whole cell or tissue lysates using Mass Spectrometry data. The package provides a shiny application to run the pipeline, several visualisations and a downloadable report of an experiment.
Authors: Bruno Contrino, Piero Ricchiuto
Maintainer: Bruno Contrino <[email protected]>
License: GPL-3
Version: 1.27.0
Built: 2024-07-13 05:04:45 UTC
Source: https://github.com/bioc/Doscheda

Help Index

Default boxplot for objects of class ChemoProtSet

Description

Description

Usage

## S4 method for signature 'ChemoProtSet'
boxplot(x, ...)

Arguments

x

object of class 'ChemoProtSet'
...

other plotting options

Value

boxplot for objects of class ChemoProtSet

An S4 class to run the doscheda pipeline

Description

An S4 class to run the doscheda pipeline

Slots

input

A data.frame containing the input data

normData

A data.frame containin a processed and standardised version of the input data

finalData

A data.frame containing the final data produced by the pipline

parameters

A list containing all the parameters required to make the pipeline run successfully

datasets

A list containing other potentially useful datasets

Plot showing correlation between all channels across replicates

Description

Plot of the correlation between all the channels in the data.

Usage

corrPlot(x, ...)

## S4 method for signature 'ChemoProtSet'
corrPlot(x, ...)

Arguments

x

object of class 'ChemoProtSet'
...

corrplot options

Value

correlation plot for objects of class ChemoProtSet

Examples

ex <- processedExample
ex <- runNormalisation(ex)
ex <- fitModel(ex)
corrPlot(ex)

Density plot for objects of class ChemoProtSet

Description

Description

Usage

densityPlot(x, rankProteins = FALSE, ...)

## S4 method for signature 'ChemoProtSet'
densityPlot(x, rankProteins = FALSE, ...)

Arguments

x

object of class 'ChemoProtSet'
rankProteins

plot a the set of ranked proteins or plot the density of the channels
...

other plot options

Value

density plot for objects of class ChemoProtSet

Examples

ex <- processedExample
ex <- runNormalisation(ex)
ex <- fitModel(ex)
densityPlot(ex)

Doscheda: A package for Down Stream Chemo-Proteomics Data Analysis

Description

The Doscheda package provides three categories of important functions: foo, bar and baz.

Foo functions

The foo functions ...

Run shiny application for DOSCHEDA

Description

Run a version of the pipline with some extra features and a simple user experience. The application is documented in detail at here

Usage

doschedaApp()

Value

Launches shiny application

Peptide Intensity data set for Doscheda

Description

A fabricated data set to run the Doscheda pipeline from peptide intensity.

Usage

data(doschedaData)

Format

An object of class data.frame with 21140 rows and 15 columns.

Examples

data(doschedaData)
head(doschedaData)

Method to fit a model to an object of class 'ChemoProtSet'

Description

Method to fit a model to an object of class 'ChemoProtSet'

Usage

fitModel(x)

## S4 method for signature 'ChemoProtSet'
fitModel(x)

Arguments

x

object of class 'ChemoProtSet'

Value

object of class ChemoProtSet

See Also

DoschedaSet

Examples

channelNames <- c('Abundance..F1..126..Control..REP_1',
'Abundance..F1..127..Sample..REP_1',  'Abundance..F1..128..Sample..REP_1',
 'Abundance..F1..129..Sample..REP_1',  'Abundance..F1..130..Sample..REP_1',
'Abundance..F1..131..Sample..REP_1',  'Abundance..F2..126..Control..REP_2',
'Abundance..F2..127..Sample..REP_2', 'Abundance..F2..128..Sample..REP_2',
'Abundance..F2..129..Sample..REP_2',  'Abundance..F2..130..Sample..REP_2',
'Abundance..F2..131..Sample..REP_2')
ex <- new('ChemoProtSet')
ex<- setParameters(x = ex,chansVal = 6, repsVal = 2,dataTypeStr = 'intensity',
 modelTypeStr = 'linear',PDBool = FALSE,removePepsBool = FALSE,
 incPDofPDBool = FALSE,incGeneFileBool = FALSE,organismStr = 'H.sapiens', pearsonThrshVal = 0.4)
ex<- setData(x = ex, dataFrame = doschedaData, dataChannels = channelNames,
accessionChannel = 'Master.Protein.Accessions',
              sequenceChannel = 'Sequence', qualityChannel = 'Qvality.PEP' )
ex <- removePeptides(ex,removePeps = FALSE)
ex <- runNormalisation(ex)
ex <- fitModel(ex)
ex

ex <- processedExample
ex <- runNormalisation(ex)
ex <- fitModel(ex)

ex

Accessor function for the datasets slot.

Description

Accessor function for the datasets slot of a ChemoProtSet object.

Usage

getDatasets(x)

## S4 method for signature 'ChemoProtSet'
getDatasets(x)

Arguments

x

object of class ChemoProtSet

Value

object of class ChemoProtSet

See Also

DoschedaSet

Examples

ex <- new('ChemoProtSet')
getDatasets(ex)

Accessor function for the finalData slot.

Description

Accessor function for the finalData slot of a ChemoProtSet object.

Usage

getFinal(x)

## S4 method for signature 'ChemoProtSet'
getFinal(x)

Arguments

x

object of class ChemoProtSet

Value

object of class ChemoProtSet

See Also

DoschedaSet

Examples

ex <- new('ChemoProtSet')
getParameters(ex)

Accessor function for the Input

Description

Accessor function for the Input slot of a ChemoProtSet object.

Usage

getInput(x)

## S4 method for signature 'ChemoProtSet'
getInput(x)

Arguments

x

object of class ChemoProtSet

Value

object of class ChemoProtSet

See Also

DoschedaSet

Examples

ex <- new('ChemoProtSet')
getInput(ex)

Accessor function for the normData

Description

Accessor function for the normData slot of a ChemoProtSet object.

Usage

getNorm(x)

## S4 method for signature 'ChemoProtSet'
getNorm(x)

Arguments

x

object of class ChemoProtSet

Value

object of class ChemoProtSet

See Also

DoschedaSet

Examples

ex <- new('ChemoProtSet')
getNorm(ex)

Accessor function for the parameters slot.

Description

Accessor function for the parameters slot of a ChemoProtSet object.

Usage

getParameters(x)

## S4 method for signature 'ChemoProtSet'
getParameters(x)

Arguments

x

object of class ChemoProtSet

Value

object of class ChemoProtSet

See Also

DoschedaSet

Examples

ex <- new('ChemoProtSet')
getParameters(ex)

Create report from 'ChemProtSet' object

Description

Genereate a report that includes several plots and descriptions for an experiment that has been anaylsed using Doscheda

Usage

makeReport(x)

Arguments

x

Object of class 'ChemoProtSet'

Value

html report of processed 'ChemoProtSet' object

Examples

## Not run: 
ex<- new('ChemoProtSet')
makeReport(ex)

## End(Not run)

MeanSd plot for objects of class ChemoProtSet

Description

Shows the ranked means with a running median calculated with a window size of 10

Usage

meanSdPlot(x, ...)

## S4 method for signature 'ChemoProtSet'
meanSdPlot(x, ...)

Arguments

x

object of class 'ChemoProtSet'
...

other plot options

Value

meanSd plot for objects of class ChemoProtSet

Examples

ex <- processedExample
ex <- runNormalisation(ex)
ex <- fitModel(ex)
meanSdPlot(ex)

PCA of the main data sets contained in a object of class ChemoProtSet

Description

Plot of Principal Component Analysis for the first two principal components of the experimental data.

Usage

pcaPlot(x, ...)

## S4 method for signature 'ChemoProtSet'
pcaPlot(x, ...)

Arguments

x

object of class 'ChemoProtSet'
...

other plot options

Value

PCA plot for objects of class ChemoProtSet

See Also

DoschedaSet

Examples

ex <- processedExample
ex <- runNormalisation(ex)
ex <- fitModel(ex)
pcaPlot(ex)
ex <- processedExample
ex <- runNormalisation(ex)
ex <- fitModel(ex)
pcaPlot(ex)

Default plot for objects of class ChemoProtSet

Description

Description

Usage

## S3 method for class 'ChemoProtSet'
plot(x, sigmoidCoef = "rb50", ...)

Arguments

x

object of class 'ChemoProtSet'
sigmoidCoef

the sigmoidal coeffcient, one of ('difference', 'slope', 'rb50'). Obselete if modelType is 'linear'
...

other plotting options

Value

plot for objects of class ChemoProtSet

Processed Peptide Intensity data set for Doscheda

Description

A processed fabricated data set to run the Doscheda pipeline from peptide intensity.

Usage

data(processedExample)

Format

An object of class ChemoProtSet of length 1.

Examples

data(processedExample)
str(processedExample)

Method to remove peptides from input data of an object of class 'ChemoProtSet'

Description

Method to remove peptides from input data of an object of class 'ChemoProtSet'

Usage

removePeptides(x, changePearson = NA, removePeps = TRUE)

## S4 method for signature 'ChemoProtSet'
removePeptides(x, changePearson = NA,
  removePeps = TRUE)

Arguments

x

object of class 'ChemoProtSet'
changePearson

option to change the peasrson threshold cut-off parameter
removePeps

boolean value indicating whether peptide removal should take place

Value

object of class ChemoProtSet

See Also

DoschedaSet

Examples

## Not run: 
channelNames <- c('Abundance..F1..126..Control..REP_1',
'Abundance..F1..127..Sample..REP_1',  'Abundance..F1..128..Sample..REP_1',
 'Abundance..F1..129..Sample..REP_1',  'Abundance..F1..130..Sample..REP_1',
'Abundance..F1..131..Sample..REP_1',  'Abundance..F2..126..Control..REP_2',
'Abundance..F2..127..Sample..REP_2', 'Abundance..F2..128..Sample..REP_2',
'Abundance..F2..129..Sample..REP_2',  'Abundance..F2..130..Sample..REP_2',
'Abundance..F2..131..Sample..REP_2')
ex <- new('ChemoProtSet')
ex<- setParameters(x = ex,chansVal = 6, repsVal = 2,
dataTypeStr = 'intensity', modelTypeStr = 'linear',
 PDBool = FALSE,removePepsBool = FALSE,incPDofPDBool = FALSE,
  incGeneFileBool = FALSE,organismStr = 'H.sapiens',
   pearsonThrshVal = 0.4)

ex<- setData(x = ex, dataFrame = doschedaData,
 dataChannels = channelNames,
 accessionChannel = 'Master.Protein.Accessions',
  sequenceChannel = 'Sequence',
  qualityChannel = 'Qvality.PEP' )
ex <- removePeptides(ex,removePeps = FALSE)
ex

## End(Not run)

Plot replicates between concentrations

Description

Plot of Fold Change between replicate i and replicate j at at a given concentration

Usage

replicatePlot(x, conc, repIndex1, repIndex2, ...)

## S4 method for signature 'ChemoProtSet'
replicatePlot(x, conc, repIndex1, repIndex2, ...)

Arguments

x

object of class 'ChemoProtSet'
conc

concentration of channel
repIndex1

index of replicate on x axis
repIndex2

index of replicate on y axis
...

options

Value

Replicate plot for objects of class ChemoProtSet

Examples

ex <- processedExample
ex <- runNormalisation(ex)
ex <- fitModel(ex)
replicatePlot(ex,0,1,2)

Wrapper Function to run the entire Doscheda pipeline

Description

A wrapper for the whole Doscheda pipeline, if users want to avoid using the separate steps.

Usage

runDoscheda(dataFrame, dataChannels, accessionChannel, chansVal, repsVal,
  dataTypeStr, modelTypeStr, PDBool = TRUE, removePepsBool = NA,
  incPDofPDBool = FALSE, PDofPDname = NA, incGeneFileBool = FALSE,
  organismStr = "h.sapiens", sigmoidConc = NA, pearsonThrshVal = 0.4,
  uniquePeps = NA, sequenceChannel = NA, qualityChannel = NA,
  pdofpdChannel = NA, incGeneID = FALSE, geneIDFile = NA,
  normType = "loess")

Arguments

dataFrame

data.frame of the input data set
dataChannels

column names of dataFrame that correspond to data channels. These should be ordered in the format: rep1_concentration_0, ..., rep1_concentration_n, rep2_concentration_0, ...
accessionChannel

string that is the same as the column name for the protein accessions in dataFrame
chansVal

number of channels / concentrations in experiment
repsVal

number of replicates in experiment
dataTypeStr

string describing the data type of input data set. This can be 'LFC' for log fold-changes, 'FC' for fold-changes and 'intensity' for peptide intensities
modelTypeStr

string describing the type of model applied. This can be 'linear' for a linear model or 'sigmoid' for a sigmoidal model
PDBool

boolean value indicating if the input data is from Proteome Discoverer 2.1 or not
removePepsBool

boolean value indicating if peptide removal will take place. Only valid if input data is peptide intensities
incPDofPDBool

boolean value indicating if the input data contais a pull-down of pull-down colum
PDofPDname

string with the same name as colulmn containing pull-down of pull-down data. NA if this is not applicable
incGeneFileBool

boolean value indicating if the data requires a protein accession to gene ID conversion file
organismStr

string giving the name of organism. the options are: 'H.sapiens', 'D. melanogaster', 'C. elegans', 'R. norvegicus', 'M. musculus'. This is only needed if PDbool is FALSE
sigmoidConc

vector of numerical values for concentrations of channels in the case of a sigmoidal fit
pearsonThrshVal

numerial value between -1 and 1 which determines the cut-off used to discard peptides during peptide removal
uniquePeps

string that is the same as the column name for the number of unique peptides in dataFrame
sequenceChannel

string that is the same as the column name for the peptide sequences in dataFrame
qualityChannel

string that is the same as the column name for the peptide quality score in dataFrame
pdofpdChannel

string that is the same as the column name for the pull-down of pull-down data in dataFrame
incGeneID

boolean value indicating if a protein accession to gene ID file is supplied
geneIDFile

data.frame containing a protein accession to gene ID conversion file
normType

string indicating the type of normalisation that should take place ('loess', 'median', 'none')

Value

object of class ChemoProtSet

See Also

DoschedaSet

Examples

channelNames <- c('Abundance..F1..126..Control..REP_1',
'Abundance..F1..127..Sample..REP_1',  'Abundance..F1..128..Sample..REP_1',
'Abundance..F1..129..Sample..REP_1',  'Abundance..F1..130..Sample..REP_1',
'Abundance..F1..131..Sample..REP_1',  'Abundance..F2..126..Control..REP_2',
'Abundance..F2..127..Sample..REP_2', 'Abundance..F2..128..Sample..REP_2',
'Abundance..F2..129..Sample..REP_2',  'Abundance..F2..130..Sample..REP_2',
'Abundance..F2..131..Sample..REP_2')

ex <- runDoscheda(dataFrame = doschedaData, dataChannels = channelNames,
chansVal = 6, repsVal = 2,dataTypeStr = 'intensity',
modelTypeStr = 'linear',PDBool = FALSE,removePepsBool = FALSE,
accessionChannel = 'Master.Protein.Accessions',
sequenceChannel = 'Sequence',qualityChannel = 'Qvality.PEP',
incPDofPDBool = FALSE, incGeneFileBool = FALSE,
 organismStr = 'H.sapiens', pearsonThrshVal = 0.4)

Method to remove peptides from input data of an object of class 'ChemoProtSet'

Description

Method to remove peptides from input data of an object of class 'ChemoProtSet'

Usage

runNormalisation(x, normalise = "loess")

## S4 method for signature 'ChemoProtSet'
runNormalisation(x, normalise = "loess")

Arguments

x

object of class 'ChemoProtSet'
normalise

string indicating the type of normalisation that should take place ('loess', 'median', 'none')

Value

object of class ChemoProtSet

See Also

DoschedaSet

Examples

ex <- processedExample
ex <- runNormalisation(ex)
ex

Method for attaching and standardising data for objects of class 'ChemoProtSet'

Description

This method will subset the orginal data set into the required columns, standardising column names in the process.

Usage

setData(x, dataFrame, dataChannels, accessionChannel, uniquePeps = NA,
  sequenceChannel = NA, qualityChannel = NA, pdofpdChannel = NA,
  incGeneID = FALSE, geneIDFile = NA)

## S4 method for signature 'ChemoProtSet'
setData(x, dataFrame, dataChannels, accessionChannel,
  uniquePeps = NA, sequenceChannel = NA, qualityChannel = NA,
  pdofpdChannel = NA, incGeneID = FALSE, geneIDFile = NA)

Arguments

x

object of class 'ChemoProtSet'
dataFrame

data.frame of the input data set
dataChannels

column names of dataFrame that correspond to data channels. These should be ordered in the format: rep1_concentration_0, ..., rep1_concentration_n, rep2_concentration_0, ...
accessionChannel

string that is the same as the column name for the protein accessions in dataFrame
uniquePeps

string that is the same as the column name for the number of unique peptides in dataFrame
sequenceChannel

string that is the same as the column name for the peptide sequences in dataFrame
qualityChannel

string that is the same as the column name for the peptide quality score in dataFrame
pdofpdChannel

string that is the same as the column name for the pull-down of pull-down data in dataFrame
incGeneID

boolean value indicating if a protein accession to gene ID file is supplied
geneIDFile

data.frame containing a protein accession to gene ID conversion file

Value

object of class ChemoProtSet

See Also

DoschedaSet

Examples

channelNames <- c('Abundance..F1..126..Control..REP_1',
'Abundance..F1..127..Sample..REP_1',  'Abundance..F1..128..Sample..REP_1',
 'Abundance..F1..129..Sample..REP_1',  'Abundance..F1..130..Sample..REP_1',
'Abundance..F1..131..Sample..REP_1',  'Abundance..F2..126..Control..REP_2',
'Abundance..F2..127..Sample..REP_2', 'Abundance..F2..128..Sample..REP_2',
'Abundance..F2..129..Sample..REP_2',  'Abundance..F2..130..Sample..REP_2',
'Abundance..F2..131..Sample..REP_2')

ex <- new('ChemoProtSet')
ex<- setParameters(x = ex,chansVal = 6, repsVal = 2,dataTypeStr = 'intensity',
modelTypeStr = 'linear',PDBool = FALSE,removePepsBool = FALSE,
incPDofPDBool = FALSE,incGeneFileBool = FALSE,organismStr = 'H.sapiens', pearsonThrshVal = 0.4)
ex<- setData(x = ex, dataFrame = doschedaData, dataChannels = channelNames,
accessionChannel = 'Master.Protein.Accessions',
sequenceChannel = 'Sequence',qualityChannel = 'Qvality.PEP')

ex

Method to set parameters for a ChemoProtSet

Description

Give the ChemoProtSet object the correct parameters for a given experiment in order to successfully run the pipelin

Usage

setParameters(x, chansVal, repsVal, dataTypeStr, modelTypeStr, PDBool = TRUE,
  removePepsBool = NA, incPDofPDBool = FALSE, PDofPDname = NA,
  incGeneFileBool = FALSE, organismStr = "h.sapiens", sigmoidConc = NA,
  pearsonThrshVal = 0.4)

## S4 method for signature 'ChemoProtSet'
setParameters(x, chansVal, repsVal, dataTypeStr,
  modelTypeStr, PDBool = TRUE, removePepsBool = NA, incPDofPDBool = FALSE,
  PDofPDname = NA, incGeneFileBool = FALSE, organismStr = "h.sapiens",
  sigmoidConc = NA, pearsonThrshVal = 0.4)

Arguments

x

object of class 'ChemoProtSet'
chansVal

number of channels / concentrations in experiment
repsVal

number of replicates in experiment
dataTypeStr

string describing the data type of input data set. This can be 'LFC' for log fold-changes, 'FC' for fold-changes and 'intensity' for peptide intensities
modelTypeStr

string describing the type of model applied. This can be 'linear' for a linear model or 'sigmoid' for a sigmoidal model
PDBool

boolean value indicating if the input data is from Proteome Discoverer 2.1 or not
removePepsBool

boolean value indicating if peptide removal will take place. Only valid if input data is peptide intensities
incPDofPDBool

boolean value indicating if the input data contais a pull-down of pull-down colum
PDofPDname

string with the same name as colulmn containing pull-down of pull-down data. NA if this is not applicable
incGeneFileBool

boolean value indicating if the data requires a protein accession to gene ID conversion file
organismStr

string giving the name of organism. the options are: 'H.sapiens', 'D. melanogaster', 'C. elegans', 'R. norvegicus', 'M. musculus'. This is only needed if PDbool is FALSE
sigmoidConc

vector of numerical values for concentrations of channels in the case of a sigmoidal fit
pearsonThrshVal

numerial value between -1 and 1 which determines the cut-off used to discard peptides during peptide removal

Value

object of class ChemoProtSet

See Also

DoschedaSet

Examples

channelNames <- c('Abundance..F1..126..Control..REP_1',
'Abundance..F1..127..Sample..REP_1',  'Abundance..F1..128..Sample..REP_1',
'Abundance..F1..129..Sample..REP_1',  'Abundance..F1..130..Sample..REP_1',
'Abundance..F1..131..Sample..REP_1',  'Abundance..F2..126..Control..REP_2',
'Abundance..F2..127..Sample..REP_2', 'Abundance..F2..128..Sample..REP_2',
'Abundance..F2..129..Sample..REP_2',  'Abundance..F2..130..Sample..REP_2',
'Abundance..F2..131..Sample..REP_2')

ex <- new('ChemoProtSet')
ex<- setParameters(x = ex,chansVal = 6, repsVal = 2,dataTypeStr = 'intensity',
modelTypeStr = 'linear',PDBool = FALSE, removePepsBool = FALSE,
incPDofPDBool = FALSE, incGeneFileBool = FALSE,
organismStr = 'H.sapiens', pearsonThrshVal = 0.4)

ex

Volcano plot for objects of class ChemoProtSet

Description

Volcano plots designed to be run on objects of class 'ChemoProtSet' when a linear model has been applied.

Usage

volcanoPlot(x, coefficient = "slope", avExprs = 0.2, pVal = 0.05, ...)

## S4 method for signature 'ChemoProtSet'
volcanoPlot(x, coefficient = "slope",
  avExprs = 0.2, pVal = 0.05, ...)

Arguments

x

object of class 'ChemoProtSet'
coefficient

coefficient of linear model to be plotted ('slope','intercept','quadratic')
avExprs

average expression cutoff
pVal

p-value cut-off
...

other plotting options

Value

volcano plot for objects of class ChemoProtSet

See Also

DoschedaSet

Examples

ex <- processedExample
ex <- runNormalisation(ex)
ex <- fitModel(ex)
volcanoPlot(ex)