# Tools for the Differential Analysis of Proteins Abundance with R

## Documentation for package ‘DaparToolshed’ version 0.99.38

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F G H I K L M N O P Q R S T U V W

## -- A --

Add2History | Add row to history
addColors | Exports a 'QFeatures' object to a Excel file.
Add_Aggregated_rowData | Aggregate metacell
Add_Item_to_Dataset | Adds an instance of 'SummarizedExperiment' to a 'QFeatures' object
adjacency-matrix-filter | Filter a peptide assay on the basis of its adjacency matrix.
AdjMatFilters | Filter a peptide assay on the basis of its adjacency matrix.
aggQmetacell | Aggregate metacell
aggregateFeatures4Prostar | Aggregate an assay's quantitative features
aggregateFeatures4Prostar-method | Aggregate an assay's quantitative features
aggregateMethods | Aggregate metacell
aggregateRedistribution | Aggregate an assay's quantitative features with shared peptide redistribution
aggregateRedistribution-method | Aggregate an assay's quantitative features with shared peptide redistribution
allPeptides | Filter a peptide assay on the basis of its adjacency matrix.
analysis | List of metacell tags
analysis-method | List of metacell tags
analysis<- | List of metacell tags
applyAnovasOnProteins | iteratively applies OWAnova() on the features of an MSnSet object

## -- B --

BuildAdjacencyMatrix | Function matrix of appartenance group
BuildColumnToProteinDataset | Aggregate metacell
buildGraph | Display a CC
BuildMetacell | Metacell function

## -- C --

checkConditions | Check if the design is valid
checkDesign | Check if the design is valid
Children | Names of all children of a node
classic1wayAnova | Function to perform a One-way Anova statistical test on a MsnBase dataset
CleanRowData | Clean row data
compareNormalizationD_HC | Builds a plot from a dataframe. Same as compareNormalizationD but uses the library 'plotly'
compute_t_tests | Compute a t-test
ConnectedComp | List of metacell tags
ConnectedComp-method | List of metacell tags
ConnectedComp<- | List of metacell tags
ConvertListToHtml | Convert a list to unnumbered HTML list
CountPep | Compute the number of peptides used to aggregate proteins
createQFeatures | Creates an object of class 'QFeatures' from text file.
createSampleinfo | Creates an object of class 'QFeatures' from text file.
custom_metacell_colors | Quantitative metadata vocabulary for entities

## -- D --

DaparToolsehd, | Filter features of one SE based on their rowData
DaparToolshed-aggregate | Aggregate an assay's quantitative features
DaparToolshed-aggregateRedistribution | Aggregate an assay's quantitative features with shared peptide redistribution
design_qf | List of metacell tags
design_qf-method | List of metacell tags
design_qf<- | List of metacell tags
diffAnaComputeAdjustedPValues | Computes the adjusted p-values
diffAnaComputeFDR | Computes the FDR corresponding to the p-values of the differential analysis
diffAnaVolcanoplot_rCharts | Volcanoplot of the differential analysis
DifferentialAnalysis | List of metacell tags
DifferentialAnalysis-method | List of metacell tags
DifferentialAnalysis<- | List of metacell tags
displayCCvisNet | Display a CC

## -- E --

ExtendPalette | Extends a base-palette of the package RColorBrewer to n colors.
ExtractUniquePeptides | Get unique peptide

## -- F --

filename | List of metacell tags
filename-method | List of metacell tags
filename<- | List of metacell tags
filterFeaturesOneSE | Filter features of one SE based on their rowData
filterFeaturesOneSE, | Filter features of one SE based on their rowData
filterFeaturesOneSE-method | Filter features of one SE based on their rowData
findMECBlock | Finds the LAPALA
formatHSDResults | Extracts the FC and the FWER ajusted p-values and format them in a data.frame
formatLimmaResult | Format Limma results
formatPHResults | Extract logFC and raw pvalues from multiple post-hoc models summaries
formatPHTResults | Extracts the FC and the raw p-values and format them in a data.frame
fudge2LRT | Heuristic to choose the value of the hyperparameter (fudge factor) used to regularize the variance estimator in the likelihood ratio statistic
FunctionFilter | Filter features of one SE based on their rowData
FunctionFilter, | Filter features of one SE based on their rowData
FunctionFilter-class | Filter features of one SE based on their rowData

## -- G --

GetColorsForConditions | Builds a complete color palette for the conditions given in argument
getDesignLevel | Get design level
GetDetailedNbPeptides | Computes the detailed number of peptides for each protein
GetDetailedNbPeptidesUsed | Computes the detailed number of peptides used for aggregating each protein
GetHistory | Wrapper for the 'paramshistory' function.
GetIndices_BasedOnConditions | Search lines which respects request on one or more conditions.
GetIndices_FunFiltering | Delete the lines in the matrix of intensities and the metadata table given their indices.
GetIndices_WholeLine | Search lines which respects query on all their elements.
GetIndices_WholeMatrix | Search lines which respects request on one or more conditions.
getListNbValuesInLines | Returns the possible number of values in lines in the data
GetMetacellTags | List of metacell tags
GetMetacellTags-method | List of metacell tags
GetMetadataSlot | List of metacell tags
GetNbPeptidesUsed | Computes the number of peptides used for aggregating each protein
GetNbTags | Number of each metacell tags
getNumberOfEmptyLines | Returns the number of empty lines in the data
getPepProtCC | Build the list of connex composant of the adjacency matrix
getProteinsStats | Computes the number of proteins that are only defined by specific peptides, shared peptides or a mixture of two.
getQuantile4Imp | Finds the LAPALA
GetRowdataSlot | List of metacell tags
GetSoftAvailables | The set of available softwares to convert from
GetUniqueTags | List of metacell tags
GetUniqueTags-method | List of metacell tags
globalAdjPval | Computes the adjusted p-values on all the stacked contrasts using CP4P
GlobalQuantileAlignment | Normalisation
GraphPepProt | Function to create a histogram that shows the repartition of peptides w.r.t. the proteins

## -- H --

hc_logFC_DensityPlot | Density plots of logFC values
hc_mvTypePlot2 | Bar plot of missing values per lines using plotly
heatmapForMissingValues | Display a heatmap for data with missing values
histPValue_HC | Plots a histogram of p-values
HypothesisTest | List of metacell tags
HypothesisTest-method | List of metacell tags
HypothesisTest<- | List of metacell tags

## -- I --

idcol | List of metacell tags
idcol-method | List of metacell tags
idcol<- | List of metacell tags
imputePA2 | Missing values imputation from a 'MSnSet' object
InitializeHistory | Initialize the history
innerAggregateIter | Aggregate metacell
innerMean | Aggregate metacell
innerMedian | Aggregate metacell
innerMedianpolish | Aggregate metacell
innerRobustsummary | Aggregate metacell
innerSum | Aggregate metacell
isDifferential | Identification of differentially abundant peptide/protein
isOfType | Similar to the function 'is.na()' but focused on the equality with the paramter 'type'.
isSubset | Check is a given set is a subset of another one.

## -- K --

Keep_Items_from_Dataset | Removes assay from a 'QFeatures' object

## -- L --

last_assay | Utility funcitons to dela with QFeatures objects.
LH0 | Compute the likelihood of the null hypothesis for the global model
LH0_lm | Compute the likelihoods of the null hypothesis for the "local" component-wise model
LH1 | Compute the likelihood of the alternative hypothesis for the global model
LH1_lm | Compute the likelihoods of the alternative hypothesis for the "local" component-wise model
limmaCompleteTest | Computes a hierarchical differential analysis
listSheets | This function exports a data.frame to a Excel file.
LOESS | Normalisation

## -- M --

mainAssay | List of metacell tags
makeContrast | Builds the contrast matrix
makeDesign | Builds the design matrix
makeDesign1 | Builds the design matrix for designs of level 1
makeDesign2 | Builds the design matrix for designs of level 2
makeDesign3 | Builds the design matrix for designs of level 3
matchMetacell | Similar to the function 'is.na()' but focused on the equality with the paramter 'type'.
MeanCentering | Normalisation
metacell-plots | Bar plot of missing values per lines using plotly
metacellDef | Quantitative metadata vocabulary for entities
MetacellFilteringScope | Lists the metacell scopes for filtering
metacellHisto_HC | Bar plot of missing values per lines using plotly
metacellPerLinesHistoPerCondition_HC | Bar plot of missing values per lines using plotly
metacellPerLinesHisto_HC | Bar plot of missing values per lines using plotly
metacell_agg | Aggregate metacell
Metacell_DIA_NN | Sets the metacell dataframe for datasets which are from Dia-NN software
Metacell_generic | Quantitative metadata vocabulary for entities
Metacell_maxquant | Sets the metacell dataframe
Metacell_proline | Sets the metacell dataframe for datasets which are from Proline software
metacombine | Quantitative metadata vocabulary for entities
mvImage | Bar plot of missing values per lines using plotly
mv_imputation_protein | Finds the LAPALA

## -- N --

NAIsZero | Set NA values to 0
names_metacell | List of metacell tags
names_metacell-method | List of metacell tags
names_metacell<- | List of metacell tags
nEmptyLines | Number of empty lines in the data
nonzero | Retrieve the indices of non-zero elements in sparse matrices
normalization_methods | Normalisation
normalizeFunction | Normalisation for QFeatures
normalizeMethods | Normalisation
n_assays_in_qf | Utility funcitons to dela with QFeatures objects.

## -- O --

output_2_Excel | This function exports a data.frame to a Excel file.
OWAnova | Applies aov() on a vector of protein abundances using the design derived from the sample names (simple aov wrapper)

## -- P --

paramshistory | List of metacell tags
paramshistory-method | List of metacell tags
paramshistory<- | List of metacell tags
Parent | Parent name of a node
parentProtId | List of metacell tags
parentProtId-method | List of metacell tags
parentProtId<- | List of metacell tags
pepaTest | PEptide based Protein differential Abundance test
Pipelines | List of available pipelines in the package
pkgsRequire | Loads packages
plotCompareAssays | Compare two assays
plotJitter | Jitter plot of CC
plotJitter_rCharts | Display a a jitter plot for CC
postHocTest | Post-hoc tests for classic 1-way ANOVA
pushpvalue | Push p-values based on metacell tags

## -- Q --

QFeatures-accessors | List of metacell tags
QFeatures-excel | Exports a 'QFeatures' object to a Excel file.
QFeatures-filtering-oneSE | Filter features of one SE based on their rowData
QFeatures-utils | Utility funcitons to dela with QFeatures objects.
QFeaturesFromSE | Utility funcitons to dela with QFeatures objects.
qMetacell | List of metacell tags
qMetacell-filter | Search lines which respects request on one or more conditions.
qMetacell-method | List of metacell tags
qMetacell<- | List of metacell tags
qMetacellFilteringScope | Search lines which respects request on one or more conditions.
qMetacellOnConditions | Search lines which respects request on one or more conditions.
qMetacellWholeLine | Search lines which respects request on one or more conditions.
qMetacellWholeMatrix | Search lines which respects request on one or more conditions.
QuantileCentering | Normalisation
q_metacell | Quantitative metadata vocabulary for entities

## -- R --

readExcel | This function exports a data.frame to a Excel file.
reIntroduceMEC | Finds the LAPALA
ReplaceSpecialChars | Standardize names
RunAggregation | Aggregation of peptide-level assay QFeatures

## -- S --

samLRT | Computes a regularized version of the likelihood ratio statistic
searchMetacellTags | Quantitative metadata vocabulary for entities
select_topn | Aggregate metacell
separateAdjPval | Computes the adjusted p-values separately on contrast using CP4P
SetHistory | Standardize names
Set_POV_MEC_tags | Quantitative metadata vocabulary for entities
Set_POV_MEC_tags2 | Quantitative metadata vocabulary for entities
sharedPeptides | Filter a peptide assay on the basis of its adjacency matrix.
specPeptides | Filter a peptide assay on the basis of its adjacency matrix.
splitAdjacencyMat | splits an adjacency matrix into specific and shared
subAdjMat_sharedPeptides | Filter a peptide assay on the basis of its adjacency matrix.
subAdjMat_specificPeptides | Filter a peptide assay on the basis of its adjacency matrix.
subAdjMat_topnPeptides | Filter a peptide assay on the basis of its adjacency matrix.
subR25pept | subR25pept dataset
subR25prot | subR25prot dataset
SumByColumns | Normalisation
SymFilteringOperators | Search lines which respects request on one or more conditions.

## -- T --

testAnovaModels | Applies a statistical test on each element of a list of linear models
testDesign | Check the validity of the design
thresholdpval4fdr | Applies p-value adjustment using cp4p on p-values below a given threshold
topnFunctions | Filter a peptide assay on the basis of its adjacency matrix.
topnPeptides | Filter a peptide assay on the basis of its adjacency matrix.
translatedRandomBeta | Generator of simulated values
typeDataset | List of metacell tags
typeDataset-method | List of metacell tags
typeDataset<- | List of metacell tags

## -- U --

UpdateMetacellAfterImputation | Quantitative metadata vocabulary for entities
UpdateMetacellAfterImputation-method | Quantitative metadata vocabulary for entities

## -- V --

VariableFilter | Filter features of one SE based on their rowData
version | List of metacell tags
version-method | List of metacell tags
version<- | List of metacell tags
vsn | Normalisation

## -- W --

wrapperCalibrationPlot | Performs a calibration plot on an 'SummarizedExperiment' object, calling the 'cp4p' package functions.
wrapperClassic1wayAnova | Wrapper for One-way Anova statistical test
wrapperDaparImputeMI | Missing values imputation using the LSimpute algorithm.
wrapperImputeDetQuant | Finds the LAPALA
wrapperImputeFixedValue | Finds the LAPALA
wrapperImputeKNN | Finds the LAPALA
wrapperImputeMLE | Imputation of peptides having no values in a biological condition.
wrapperImputePA | Finds the LAPALA
wrapperImputePA2 | Missing values imputation from a 'SummarizedExperiment' object
wrapperImputeSLSA | Finds the LAPALA
wrapperMVImage | Bar plot of missing values per lines using plotly
wrapperPirat | Missing values imputation using Pirat
write2excel | Exports a 'QFeatures' object to a Excel file.
write2excel-method | Exports a 'QFeatures' object to a Excel file.
write2excelSE | Exports a 'QFeatures' object to a Excel file.
writeExcel | This function exports a data.frame to a Excel file.
WriteHistory | This function exports a data.frame to a Excel file.
write_Assay_To_Excel | This function exports a data.frame to a Excel file.
Write_RowData | This function exports a data.frame to a Excel file.
Write_SamplesData_to_Excel | This function exports a data.frame to a Excel file.