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

AnnotationCondition Map
annotationColumnsAnnotation Columns
configurationPlotPeptidesextracts the relevant information from the configuration to... of 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
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.