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

AnnotationCondition Map
annotationColumnsAnnotation Columns
configurationPlotPeptidesextracts the relevant information from the configuration to...
contrasts.fit.NAversion of limma::contrast.fit which is able to handle NA's...
correlatedPeptideListList with peptide intensities
eb.fitfit limma
fgcz_render_One2OneReportperform rendering
fix_PD_inputFilesmassage PD inputFiles.txt - remove columns and fix column...
fixScaffoldQuantReportfix scaffold file (utility function)
getConditionColumnsget required columns for analysis
getIDLabelsid lables for piw
getIntensitiesextracts Intensity columns
getPValsget topTables for all coefficients from a limma lmfit ebayes...
getRequiredColumnsget required columns for analysis
Grp2Analysis-classPerform 2 group analysis with visualization
mergeLimmEBayesResultmerges results produced by multigroupEBaysQvalue
MQtoMSstatsFormatMaxQtoMSstatsFormat
MSstatsMappingmapping of MSStats file names
multigroupEBaysQvalueruns limma and computes qvalues
PeptideTable-classPeptide table
piwotPiwpiwots light
plotNicelyMake nice plots of transitions or peptides with correlations
plotPeptidesPlot peptide and fragments
proteinColumnsProtein Columns
ProteinTable-classProtein Table
ProteinTableR6Protein Table
QCProteinReport-classPerform 2 group analysis with visualization
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...
SRMService-classR access to Bibliospec File
summariseQValuesCompute QValue summaries for each precursor
summarizeProteinsLight only version.
tidyMQ_ProteinGroupsextract intensities and annotations from MQ proteinGroups.txt
transitionCorrelationsCompute correlation matrix
transitionCorrelationsJackCompute correlation matrix with jack
TransitionTable-classTransition table
protViz/SRMService documentation built on April 14, 2018, 7:05 a.m.