Man pages for protViz/SRMService
Report Quantitative Mass Spectrometry Data

AnnotationCondition Map
annotationColumnsAnnotation Columns
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)
genericQuantMatrixGRP2Grp2Analysis reference class for running 2 grp analysis
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
grp2PullDownExampleGrp2Analysis on pulldown data example
mergeLimmEBayesResultmerges results produced by multigroupEBaysQvalue
mqQuantMatrixGRP2Grp2Analysis on of nockout with missing data
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
proteinColumnsProtein Columns
ProteinTable-classProtein Table
ProteinTableR6Protein Table
ProteinVariableSelectWraps 4 column matrix, with Condition, Run, Protein,...
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
transitionCorrelationsCompute correlation matrix
transitionCorrelationsJackCompute correlation matrix with jack
TransitionTable-classTransition table
protViz/SRMService documentation built on Oct. 4, 2018, 12:27 a.m.