Man pages for protViz/SRMService
Performs Service SRM and LFQ analysis

aggregateTopNIntensitiesaggregates top N intensities
AnalysisConfigurationAnalysis Configuration
AnalysisParametersAnalysis parameters
AnalysisTableAnnotationCreate Annotation
AnnotationCondition Map
annotationColumnsAnnotation Columns
contrasts.fit.NAversion of limma::contrast.fit which is able to handle NA's...
correlatedPeptideListList with peptide intensities
craeteSkylineConfigurationThis function sets up an example configuration
decorelatedPlyfinds decorrelated measues
eb.fitfit limma
extractIntensitiesExtract intensity column
fgcz_render_One2OneReportperform rendering
fix_PD_inputFilesmassage PD inputFiles.txt - remove columns and fix column...
fixScaffoldQuantReportfix scaffold file (utility function)
gatherItBackmake it long
genericQuantMatrixGRP2Grp2Analysis reference class for running 2 grp analysis
getConditionColumnsget required columns for analysis
getIDLabelsid lables for piw
getIntensitiesextracts Intensity columns
getMissingStatscompute missing statistics
getPValsget topTables for all coefficients from a limma lmfit ebayes...
getRequiredColumnsget required columns for analysis
Grp2Analysis-classPerform 2 group analysis with visualization
hierarchyCountsCount distinct elements for each level of hierarchy
impute_correlationBasedimputation based on correlation assumption
linePlotHierarchy_configurationextracts the relevant information from the configuration to...
linePlotHierarchy_defaultPlot peptide and fragments
linePlotHierarchy_QuantLinemake some nice plot with summary statistics
markDecorrelatedmarks decorrelated elements
medpolishPlycompute tukeys median polish from peptide or precursor...
mergeLimmEBayesResultmerges results produced by multigroupEBaysQvalue
missignessHistogramHistogram summarizing missigness
missingPerConditionSummarize missing in condtion as barplot
missingPerConditionCumsumcumulative sums of missing
MQtoMSstatsFormatMaxQtoMSstatsFormat
MSstatsMappingmapping of MSStats file names
multigroupEBaysQvalueruns limma and computes qvalues
nr_B_in_ACompute nr of B per A
PeptideTable-classPeptide table
piwotPiwpiwots light
plotNicelyMake nice plots of transitions or peptides with correlations
proteinColumnsProtein Columns
ProteinTable-classProtein Table
ProteinTableR6Protein Table
ProteinVariableSelectWraps 4 column matrix, with Condition, Run, Protein,...
QCProteinReport-classPerform 2 group analysis with visualization
R6extractValuesHelper function to extract all value slots in an R6 object
rankPrecursorsByIntensityranks precursor - peptide by intensity.
rankPrecursorsByNAsRanks precursors by NAs (adds new column .NARank)
reestablishConditionrealign data
remap_PD_ProteinTableremap pd proteins to format compatible with grp2Analysis...
RMD_LibraryGen_specLProzorCopies the RMD and Run R file for Library generation your...
RMD_MQ_Quant_2GrpAnalysiscopies the RMD and Run files for 2 grp analysis based on MQ...
RMD_MQ_Quant_QCReportcopies the RMD and Run files for the QuantQCReport in your...
RMD_PD_Quant_2GrpAnalysiscopies the RMD and Run files for 2 grp analysis based on a PD...
RMD_QC1To1_OldCopies the Rnw file and Run R file for old 1To1 QC into your...
RMD_SRM_QC_NormalizationCopies the Rnw file and Run R file for the SRM QC and...
RMD_VarSelectionCopies the RMD and Run files for variable selection into your...
sample_analysisA data frame wich goes along with the skylineconfig and was...
sample_analysis_HLA data frame wich goes along with the skylineconfig_HL.
setIntensitiesToNAsets intensities to NA if maxQValue_Threshold exceeded
setup_analysisExtracts columns relevant for a configuration from a data...
setupDataFrameDeprecated
skylineconfigA configuration which matches the sample_analysis data.
skylineconfig_HLA configuration which matches the sample_analysis data.
skylinePRMSampleDataData frame which can be transformed into sample_analysis by...
skylineSRM_HL_dataData frame with a skyline export for an heavy to light...
spectronautDIAData250Data frame of a Spectronaut export with DIA datat
spreadValueVarsIsotopeLabelspreads isotope label heavy light into two columns
SRMService-classR access to Bibliospec File
summariseNAsadd number of NA's per lowest hierarchy to data
summariseQValuesCompute QValue summaries for each precursor
summarizeHierarchySummarize peptide Counts
summarizeProteinsLight only version. Summarize Protein counts
tidyMQ_Peptidesparse MQ peptides.txt
tidyMQ_ProteinGroupsextract intensities and annotations from MQ proteinGroups.txt
toWidetransform long to wide
toWideConfigtransform long to wide
transitionCorrelationsCompute correlation matrix
transitionCorrelationsJackCompute correlation matrix with jack
TransitionTable-classTransition table
protViz/SRMService documentation built on July 10, 2018, 12:44 p.m.