Man pages for samWieczorek/DAPAR2
Tools for the Differential Analysis of Proteins Abundance with R

Add_Item_to_Datasetxxx
adjacency-matrix-filterFilter a peptide assay on the basis of its adjacency matrix.
aggregateIterxxxx
aggregateIterParallelxxxx
aggregateMeanCompute the intensity of proteins as the mean of the...
AggregateMetacellSymbolic product of matrices
aggregateSumCompute the intensity of proteins with the sum of the...
aggregateTopnCompute the intensity of proteins as the sum of the...
BuildAdjacencyMatrixFunction matrix of appartenance group
BuildColumnToProteinDatasetcreates a column for the protein dataset after agregation by...
build-designxxxx
buildGraphDisplay a CC
BuildMetaCellmetacell function which xxx
check.conditionsCheck if the design is valid
check.designCheck if the design is valid
ChildrenNames of all chidren of a node
ConvertListToHtmlConvert a list to unnumbered HTML list
CountPepCompute the number of peptides used to aggregate proteins
create-exampleCreates an example dataset
DaparToolshedDaparToolshed: A package for computating the notorious bar...
DaparToolshed-aggregateAggregate an assay's quantitative features
design-examplexxxx
display.CC.visNetDisplay a CC
dlmod_dl
ExtendPaletteExtends a base-palette of the package RColorBrewer to n...
finalizeAggregationFinalizes the aggregation process
ftft dataset
ft_naft_na dataset
fudge2LRTHeuristic to choose the value of the hyperparameter (fudge...
GetColorsForConditionsBuilds a complete color palette for the conditions given in...
GetDetailedNbPeptidesComputes the detailed number of peptides for each protein
GetDetailedNbPeptidesUsedComputes the detailed number of peptides used for aggregating...
getExtensionExtension of a file
getListNbValuesInLinesReturns the possible number of values in lines in the data
GetMetacellxxxx
GetNbPeptidesUsedComputes the number of peptides used for aggregating each...
get.pep.prot.ccBuild the list of connex composant of the adjacency matrix
getProteinsStatsComputes the number of proteins that are only defined by...
GetSoftAvailablesThe set of available softwares to convert from
GraphPepProtFunction to create a histogram that shows the repartition of...
import-export-QFeaturesCreates an object of class 'QFeatures' from text file.
inner.aggregate.iterxxxx
inner.aggregate.topnxxxx
inner.meanxxxx
inner.sumxxxx
is.OfTypeSimilar to the function 'is.na()' but focused on the equality...
Keep_Items_from_Datasetxxx
LH0xxxxxx
LH0.lmxxxxxx
LH1xxxxxx
LH1.lmxxxxxx
match.metacellSimilar to the function 'is.na()' but focused on the equality...
Metacell_DIA_NNSets the metacell dataframe for datasets which are from...
Metacell_maxquantSets the metacell dataframe
metacell-plotsDisplays a correlation matrix of the quantitative data of a...
Metacell_prolineSets the metacell dataframe for datasets which are from...
metacell-treeDisplays a correlation matrix of the quantitative data of a...
mod_AgregationModule agregation
mod_convertxxx
mod_filterExamplexxx
mod_FilteringModule Filtering
mod_format_DTmod_format_DT_ui and mod_format_DT_server
mod_helpPopoverHelp popover windows
mod_infos_datasetmod_infos_dataset_ui and mod_infos_dataset_server
mod_inputGroupHelp popover windows
mod_open_datasetmod_open_dataset_ui and mod_open_dataset_server
mod_open_demo_datasetmod_open_demo_dataset_ui and mod_open_demo_dataset_server
mod_settingsmod_settings_ui and mod_settings_server
my_hc_chartCustomised resetZoomButton of highcharts plots
my_hc_ExportMenuCustomised contextual menu of highcharts plots
nEmptyLinesNumber of empty lines in the data
nonzeroRetrieve the indices of non-zero elements in sparse matrices
ParentParent name of a node
pepa.testPEptide based Protein differential Abundance test
pipeline-proteinModule of Protein pipeline
Pipelinesxxx
pkgs.requireLoads packages
plotJitterJitter plot of CC
plotJitter_rChartsDisplay a a jitter plot for CC
ProstarVersionsVersion number of Prostar suite
QFeatures-accessorsList of metacell tags
QFeatures-excelExports a 'QFeatures' object to a Excel file.
QFeatures-filtering-oneSEFilter features of one SE based on their rowData
QFeatures-utilsUtility funcitons to dela with QFeatures objects.
q_metacellQuantitative metadata vocabulary for entities
qMetacell-filterSearch lines which respects request on one or more...
query-metacellxxxx
query_qMetacellBuild queries for filtering quantitative metadata
ReplaceSpecialCharsStandardize names
samLRTxxxxxx
splitAdjacencyMatsplits an adjacency matrix into specific and shared
test.designCheck if xxxxxx
trackingTracking of entities within plots
samWieczorek/DAPAR2 documentation built on Oct. 15, 2023, 1:45 p.m.