Files in PTXQC

Quality Report Generation for MaxQuant and mzTab Results

README.md R/fcn_miscGGplot.R R/fcn_QCHeat.R R/fcn_plots.R R/fcn_qualities.R R/fcn_MQalign.R R/modsToTableByRaw.R R/createReport.R R/qcMetric_MSMS.R R/MzQC_classes.R R/PTXQC.R R/qcMetric_EVD.R R/mzQC.R R/MQDataReader.R R/modsToTable.R R/qcMetric.R R/fcn_PCA.R R/qcMetric_MSMSScans.R R/qcMetric_SM.R R/pkg_internal.R R/MzTabReader.R R/fcn_MQ.R R/qcMetric_EVD_modTable.R R/PTXQC-package.R R/fcn_mqpar.R R/plot_peptideMods.R R/FilenameMapper.R R/qcMetric_PG.R R/qcMetric_PAR.R R/YAMLClass.R R/createYaml.R R/fcn_misc.R inst/doc/PTXQC-Input_And_Output_Data.R inst/doc/PTXQC-Basic_Guide_for_R_users.R inst/doc/PTXQC-ListOfMetrics.Rmd inst/doc/PTXQC-Basic_Guide_for_R_users.Rmd inst/doc/PTXQC-ListOfMetrics.R inst/doc/PTXQC-FAQ.Rmd inst/doc/PTXQC-CustomizeReport.Rmd inst/doc/PTXQC-Input_And_Output_Data.Rmd inst/doc/PTXQC-DragNDrop.Rmd inst/reportTemplate/PTXQC_report_template.Rmd inst/examples/README.md inst/examples/report_v1.1.0__txt_5files_withMatch-100min.pdf inst/dragNdrop/README.md inst/dragNdrop/QC-dragdrop/_internal/compute_QC_report.R tests/testthat.R tests/testthat/test_qcMetric.R tests/testthat/test_modsToTable.R tests/testthat/test_modsToTableByRaw.R tests/testthat/test_misc.R tests/testthat/test_qualities.R tests/testthat/test_computeQC.R tests/testthat/test_createYaml.R vignettes/PTXQC-ListOfMetrics.Rmd vignettes/PTXQC-Basic_Guide_for_R_users.Rmd vignettes/PTXQC-FAQ.Rmd vignettes/PTXQC-CustomizeReport.Rmd vignettes/PTXQC-Input_And_Output_Data.Rmd vignettes/PTXQC-DragNDrop.Rmd man/pasten.Rd man/getQCHeatMap.Rd man/PTXQC-package.Rd man/plot_IonInjectionTimeOverRT.Rd man/byX.Rd man/plot_CalibratedMSErr.Rd man/lcsCount.Rd man/read.MQ.Rd man/byXflex.Rd man/plot_ContUserScore.Rd man/checkEnglishLocale.Rd man/getFragmentErrors.Rd man/plot_RTPeakWidth.Rd man/pastet.Rd man/plot_peptideMods.Rd man/MQDataReader-class.Rd man/flattenList.Rd man/LCS.Rd man/plot_MS2Oversampling.Rd man/qualCentered.Rd man/repEach.Rd man/getMaxima.Rd man/supCount.Rd man/plot_MBRgain.Rd man/qualGaussDev.Rd man/getMetaData.Rd man/FilenameMapper-class.Rd man/shortenStrings.Rd man/plot_IDsOverRT.Rd man/theme_blank.Rd man/plot_RatiosPG.Rd man/simplifyNames.Rd man/wait_for_writable.Rd man/getReportFilenames.Rd man/computeMatchRTFractions.Rd man/getAbundanceClass.Rd man/appendEnv.Rd man/modsToTableByRaw.Rd man/getHTMLTable.Rd man/scale01linear.Rd man/qcMetric-class.Rd man/printWithFooter.Rd man/createReport.Rd man/inMatchWindow.Rd man/scale_y_discrete_reverse.Rd man/ScoreInAlignWindow.Rd man/print.PTXQC_table.Rd man/plot_Charge.Rd man/plot_CountData.Rd man/renameFile.Rd man/thinOutBatch.Rd man/grapes-plus-grapes.Rd man/correctSetSize.Rd man/getFileEncoding.Rd man/darken.Rd man/qcMetric_MSMSScans_TopNoverRT-class.Rd man/findAlignReference.Rd man/plot_ContsPG.Rd man/plot_TopN.Rd man/qualLinThresh.Rd man/plot_TopNoverRT.Rd man/plot_ScanIDRate.Rd man/qualCenteredRef.Rd man/plot_MBRAlign.Rd man/ggText.Rd man/brewer.pal.Safe.Rd man/grepv.Rd man/scale_x_discrete_reverse.Rd man/qualUniform.Rd man/del0.Rd man/assembleMZQC.Rd man/MzTabReader-class.Rd man/assignBlocks.Rd man/plotTable.Rd man/getMQPARValue.Rd man/getProteinCounts.Rd man/delLCS.Rd man/plot_MS2Decal.Rd man/ggAxisLabels.Rd man/getRunQualityTemplate.Rd man/RTalignmentTree.Rd man/peakWidthOverTime.Rd man/idTransferCheck.Rd man/peakSegmentation.Rd man/qualBestKS.Rd man/RSD.Rd man/plot_MBRIDtransfer.Rd man/longestCommonPrefix.Rd man/plot_IDRate.Rd man/longestCommonSuffix.Rd man/plot_MissedCleavages.Rd man/plot_ContEVD.Rd man/plot_DataOverRT.Rd man/lcpCount.Rd man/createYaml.Rd man/thinOut.Rd man/CV.Rd man/getPeptideCounts.Rd man/boxplotCompare.Rd man/YAMLClass-class.Rd man/getMetricsObjects.Rd man/alignmentCheck.Rd man/plot_ContUser.Rd man/fixCalibration.Rd man/pointsPutX.Rd man/plot_TIC.Rd man/mosaicize.Rd man/getPCA.Rd man/LCSn.Rd man/modsToTable.Rd man/qualMedianDist.Rd man/plot_UncalibratedMSErr.Rd man/QCMetaFilenames.Rd man/qualHighest.Rd man/plotTableRaw.Rd man/delLCP.Rd man/getECDF.Rd