{ "_id": "6a117103acfb0bcc41cf70b6", "Package": "PTXQC", "Type": "Package", "Title": "Quality Report Generation for MaxQuant and mzTab Results", "Version": "1.1.5", "Date": "2026-04-20", "Authors@R": "c(person(given = \"Chris\",\nfamily = \"Bielow\",\nrole = c(\"aut\", \"cre\"),\nemail = \"chris.bielow@bsc.fu-berlin.de\"),\nperson(given = \"Juliane\",\nfamily = \"Schmachtenberg\",\nrole = \"ctb\"),\nperson(given = \"Swenja\",\nfamily = \"Wagner\",\nrole = \"ctb\"),\nperson(given = \"Patricia\",\nfamily = \"Scheil\",\nrole = \"ctb\"),\nperson(given = \"Tom\",\nfamily = \"Waschischek\",\nrole = \"ctb\"),\nperson(given = \"Guido\",\nfamily = \"Mastrobuoni\",\nrole = c(\"dtc\", \"rev\")))", "Description": "Generates Proteomics (PTX) quality control (QC) reports\nfor shotgun LC-MS data analyzed with the MaxQuant software\nsuite (from .txt files) or mzTab files (ideally from OpenMS\n'QualityControl' tool). Reports are customizable (target\nthresholds, subsetting) and available in HTML or PDF format.\nPublished in J. Proteome Res., Proteomics Quality Control:\nQuality Control Software for MaxQuant Results (2015)\n.", "SystemRequirements": "pandoc (http://pandoc.org) for building Vignettes\nand output reports as HTML", "VignetteBuilder": "knitr", "License": "BSD_3_clause + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list()", "RoxygenNote": "7.3.2", "URL": "https://github.com/cbielow/PTXQC", "BugReports": "https://github.com/cbielow/PTXQC/issues", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libxml2-dev\nlibssl-dev libnode-dev zlib1g-dev", "Repository": "https://cbielow.r-universe.dev", "Date/Publication": "2026-04-23 13:34:42 UTC", "RemoteUrl": "https://github.com/cbielow/ptxqc", "RemoteRef": "HEAD", "RemoteSha": "74d48b81b744547c53b2fc383704c141ec176df5", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-23 09:13:22 UTC", "User": "root" }, "Author": "Chris Bielow [aut, cre],\nJuliane Schmachtenberg [ctb],\nSwenja Wagner [ctb],\nPatricia Scheil [ctb],\nTom Waschischek [ctb],\nGuido Mastrobuoni [dtc, rev]", "Maintainer": "Chris Bielow ", "MD5sum": "a3f4b87ab04f172e2a8e24298246ffb4", "_user": "cbielow", "_type": "src", "_file": "PTXQC_1.1.5.tar.gz", "_fileid": "573cbf63001f1ecb313e80dff9b8105aa87b8650ac4b54e1f12139afaed37001", "_filesize": 2627041, "_sha256": "573cbf63001f1ecb313e80dff9b8105aa87b8650ac4b54e1f12139afaed37001", "_created": "2026-05-23T09:13:22.000Z", "_published": "2026-05-23T09:18:59.672Z", "_distro": "noble", "_jobs": [ { "job": 77511672069, "time": 235, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7175897565" }, { "job": 77511672085, "time": 217, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7175895967" }, { "job": 77511672068, "time": 236, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7175899703" }, { "job": 77511672071, "time": 188, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7175893470" }, { "job": 77511478152, 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"longestCommonSuffix", "modsToTable", "modsToTableByRaw", "mosaicize", "pasten", "pastet", "peakWidthOverTime", "plot_CalibratedMSErr", "plot_Charge", "plot_ContEVD", "plot_ContsPG", "plot_ContUser", "plot_ContUserScore", "plot_CountData", "plot_DataOverRT", "plot_IDRate", "plot_IDsOverRT", "plot_IonInjectionTimeOverRT", "plot_MBRAlign", "plot_MBRgain", "plot_MBRIDtransfer", "plot_MissedCleavages", "plot_MS2Decal", "plot_MS2Oversampling", "plot_peptideMods", "plot_RatiosPG", "plot_RTPeakWidth", "plot_ScanIDRate", "plot_TIC", "plot_TopN", "plot_TopNoverRT", "plot_UncalibratedMSErr", "plotTable", "pointsPutX", "QCMetaFilenames", "qcMetric", "qualBestKS", "qualCentered", "qualCenteredRef", "qualGaussDev", "qualHighest", "qualLinThresh", "qualMedianDist", "qualUniform", "read.MQ", "renameFile", "repEach", "RTalignmentTree", "shortenStrings", "simplifyNames", "supCount", "theme_blank", "YAMLClass" ], "_help": [ { "page": "PTXQC-package", "title": "PTXQC: A package for computing Quality Control (QC) metrics for Proteomics (PTX)", "topics": [ "PTXQC-package" ] }, { "page": "grapes-plus-grapes", "title": "A string concatenation function, more readable than 'paste()'.", "topics": [ "%+%" ] }, { "page": "alignmentCheck", "title": "Verify an alignment by checking the retention time differences of identical peptides across Raw files", "topics": [ "alignmentCheck" ] }, { "page": "appendEnv", "title": "Add the value of a variable to an environment (fast append)", "topics": [ "appendEnv" ] }, { "page": "assembleMZQC", "title": "Collects all 'mzQC' members from each entry in lst_qcMetrics and stores them in an overall mzQC object, which can be written to disk (see writeMZQC()) or augmented otherwise", "topics": [ "assembleMZQC" ] }, { "page": "assignBlocks", "title": "Assign set numbers to a vector of values.", "topics": [ "assignBlocks" ] }, { "page": "boxplotCompare", "title": "Boxplots - one for each condition (=column) in a data frame.", "topics": [ "boxplotCompare" ] }, { "page": "brewer.pal.Safe", "title": "Return color brew palettes, but fail hard if number of requested colors is larger than the palette is holding.", "topics": [ "brewer.pal.Safe" ] }, { "page": "byX", "title": "Calls FUN on a subset of data in blocks of size 'subset_size' of unique indices.", "topics": [ "byX" ] }, { "page": "byXflex", "title": "Same as 'byX', but with more flexible group size, to avoid that the last group has only a few entries (<50% of desired size).", "topics": [ "byXflex" ] }, { "page": "checkEnglishLocale", "title": "When MaxQuant is run with a wrong locale (i.e. the decimal separator is not a '.', but a ','), then MaxQuant results are plainly wrong and broken. The can be detected by, e.g. checking for negative charge annotation", "topics": [ "checkEnglishLocale" ] }, { "page": "computeMatchRTFractions", "title": "Combine several data structs into a final picture for segmentation incurred by 'Match-between-runs'.", "topics": [ "computeMatchRTFractions" ] }, { "page": "correctSetSize", "title": "Re-estimate a new set size to split a number of items into equally sized sets.", "topics": [ "correctSetSize" ] }, { "page": "createReport", "title": "Create a quality control report (in PDF format).", "topics": [ "createReport" ] }, { "page": "createYaml", "title": "Creates a yaml file storing the parameters that are used for creating the PTXQC report and returns these parameters as well as a list of available qc-Metrics objects.", "topics": [ "createYaml" ] }, { "page": "CV", "title": "Coefficient of variation (CV)", "topics": [ "CV" ] }, { "page": "darken", "title": "Make a color (given as name or in RGB) darker by factor x = [0 = black, 1=unchanged]", "topics": [ "darken" ] }, { "page": "del0", "title": "Replace 0 with NA in a vector", "topics": [ "del0" ] }, { "page": "delLCP", "title": "Removes the longest common prefix (LCP) from a vector of strings.", "topics": [ "delLCP" ] }, { "page": "delLCS", "title": "Removes the longest common suffix (LCS) from a vector of strings.", "topics": [ "delLCS" ] }, { "page": "FilenameMapper-class", "title": "Make sure to call $readMappingFile(some_file) if you want to support a user-defined file mapping. Otherwise, calls to $getShortNames() will create/augment the mapping for filenames.", "topics": [ "FilenameMapper", "FilenameMapper-class" ] }, { "page": "findAlignReference", "title": "Return list of raw file names which were reported by MaxQuant as reference point for alignment.", "topics": [ "findAlignReference" ] }, { "page": "fixCalibration", "title": "Detect (and fix) MaxQuant mass recalibration columns, since they sometimes report wrong values.", "topics": [ "fixCalibration" ] }, { "page": "flattenList", "title": "Flatten lists of lists with irregular depths to just a list of items, i.e. a list of the leaves (if you consider the input as a tree).", "topics": [ "flattenList" ] }, { "page": "getAbundanceClass", "title": "Assign a relative abundance class to a set of (log10) abundance values", "topics": [ "getAbundanceClass" ] }, { "page": "getECDF", "title": "Estimate the empirical density and return it", "topics": [ "getECDF" ] }, { "page": "getFileEncoding", "title": "Determine if a file is 'UTF-8' or 'UTF-8-BOM' (as of MQ2.4) or 'UTF-16BE' or 'UTF-16LE'", "topics": [ "getFileEncoding" ] }, { "page": "getFragmentErrors", "title": "Extract fragment mass deviation errors from a data.frame from msms.txt", "topics": [ "getFragmentErrors" ] }, { "page": "getHTMLTable", "title": "Create an HTML table with an extra header row", "topics": [ "getHTMLTable" ] }, { "page": "getMaxima", "title": "Find the local maxima in a vector of numbers.", "topics": [ "getMaxima" ] }, { "page": "getMetaData", "title": "Extract meta information (orderNr, metric name, category) from a list of Qc metric objects", "topics": [ "getMetaData" ] }, { "page": "getMetaFilenames", "title": "Parses the given mqpar.xml file (or, if not found, tries the 'txt_folder' + '/../../' folder (i.e. where the raw data should be)) to extract the full filepaths for all Raw files", "topics": [ "getMetaFilenames" ] }, { "page": "getMetricsObjects", "title": "Get all currently available metrics", "topics": [ "getMetricsObjects" ] }, { "page": "getMQPARValue", "title": "Retrieve a parameter value from a mqpar.xml file", "topics": [ "getMQPARValue" ] }, { "page": "getPCA", "title": "Create a principal component analysis (PCA) plot for the first two dimensions.", "topics": [ "getPCA" ] }, { "page": "getPeptideCounts", "title": "Extract the number of peptides observed per Raw file from an evidence table.", "topics": [ "getPeptideCounts" ] }, { "page": "getProteinCounts", "title": "Extract the number of protein groups observed per Raw file from an evidence table.", "topics": [ "getProteinCounts" ] }, { "page": "getQCHeatMap", "title": "Generate a Heatmap from a list of QC measurements.", "topics": [ "getQCHeatMap" ] }, { "page": "getReportFilenames", "title": "Assembles a list of output file names, which will be created during reporting.", "topics": [ "getReportFilenames" ] }, { "page": "getRunQualityTemplate", "title": "Get an mzQC runQuality without actual metrics, but with full metadata", "topics": [ "getRunQualityTemplate" ] }, { "page": "ggAxisLabels", "title": "Function to thin out the number of labels shown on an axis in GGplot", "topics": [ "ggAxisLabels" ] }, { "page": "ggText", "title": "Plot a text as graphic using ggplot2.", "topics": [ "ggText" ] }, { "page": "grepv", "title": "Grep with values returned instead of indices.", "topics": [ "grepv" ] }, { "page": "idTransferCheck", "title": "Check how close transferred ID's after alignment are to their genuine IDs within one Raw file.", "topics": [ "idTransferCheck" ] }, { "page": "inMatchWindow", "title": "For grouped peaks: separate them into in-width vs. out-width class.", "topics": [ "inMatchWindow" ] }, { "page": "lcpCount", "title": "Count the number of chars of the longest common prefix", "topics": [ "lcpCount" ] }, { "page": "LCS", "title": "Compute longest common substring of two strings.", "topics": [ "LCS" ] }, { "page": "lcsCount", "title": "Count the number of chars of the longest common suffix", "topics": [ "lcsCount" ] }, { "page": "LCSn", "title": "Find longest common substring from 'n' strings.", "topics": [ "LCSn" ] }, { "page": "longestCommonPrefix", "title": "Get the longest common prefix from a set of strings.", "topics": [ "longestCommonPrefix" ] }, { "page": "longestCommonSuffix", "title": "Like longestCommonPrefix(), but on the suffix.", "topics": [ "longestCommonSuffix" ] }, { "page": "modsToTable", "title": "Convert list of (mixed)modifications to a frequency table", "topics": [ "modsToTable" ] }, { "page": "modsToTableByRaw", "title": "Convert list of (mixed)modifications to a frequency table", "topics": [ "modsToTableByRaw" ] }, { "page": "mosaicize", "title": "Prepare a Mosaic plot of two columns in long format.", "topics": [ "mosaicize" ] }, { "page": "MQDataReader-class", "title": "S5-RefClass to read MaxQuant .txt files", "topics": [ "MQDataReader", "MQDataReader-class" ] }, { "page": "MzTabReader-class", "title": "Class to read an mzTab file and store the tables internally.", "topics": [ "MzTabReader", "MzTabReader-class" ] }, { "page": "pasten", "title": "paste with newline as separator", "topics": [ "pasten" ] }, { "page": "pastet", "title": "paste with tab as separator", "topics": [ "pastet" ] }, { "page": "peakSegmentation", "title": "Determine fraction of evidence which causes segmentation, i.e. sibling peaks at different RTs confirmed either by genuine or transferred MS/MS.", "topics": [ "peakSegmentation" ] }, { "page": "peakWidthOverTime", "title": "Discretize RT peak widths by averaging values per time bin.", "topics": [ "peakWidthOverTime" ] }, { "page": "plot_CalibratedMSErr", "title": "Plot bargraph of uncalibrated mass errors for each Raw file.", "topics": [ "plot_CalibratedMSErr" ] }, { "page": "plot_Charge", "title": "The plots shows the charge distribution per Raw file. The output of 'mosaicize()' can be used directly.", "topics": [ "plot_Charge" ] }, { "page": "plot_ContEVD", "title": "Plot contaminants from evidence.txt, broken down into top5-proteins.", "topics": [ "plot_ContEVD" ] }, { "page": "plot_ContsPG", "title": "Plot contaminants from proteinGroups.txt", "topics": [ "plot_ContsPG" ] }, { "page": "plot_ContUser", "title": "Plot user-defined contaminants from evidence.txt", "topics": [ "plot_ContUser" ] }, { "page": "plot_ContUserScore", "title": "Plot Andromeda score distribution of contaminant peptide vs. matrix peptides.", "topics": [ "plot_ContUserScore" ] }, { "page": "plot_CountData", "title": "Plot Protein groups per Raw file", "topics": [ "plot_CountData" ] }, { "page": "plot_DataOverRT", "title": "Plot some count data over time for each Raw file.", "topics": [ "plot_DataOverRT" ] }, { "page": "plot_IDRate", "title": "Plot percent of identified MS/MS for each Raw file.", "topics": [ "plot_IDRate" ] }, { "page": "plot_IDsOverRT", "title": "Plot IDs over time for each Raw file.", "topics": [ "plot_IDsOverRT" ] }, { "page": "plot_IonInjectionTimeOverRT", "title": "Plot line graph of TopN over Retention time.", "topics": [ "plot_IonInjectionTimeOverRT" ] }, { "page": "plot_MBRAlign", "title": "Plot MaxQuant Match-between-runs alignment performance.", "topics": [ "plot_MBRAlign" ] }, { "page": "plot_MBRgain", "title": "Plot MaxQuant Match-between-runs id transfer performance as a scatterplot.", "topics": [ "plot_MBRgain" ] }, { "page": "plot_MBRIDtransfer", "title": "Plot MaxQuant Match-between-runs id transfer performance.", "topics": [ "plot_MBRIDtransfer" ] }, { "page": "plot_MissedCleavages", "title": "Plot bargraph of missed cleavages.", "topics": [ "plot_MissedCleavages" ] }, { "page": "plot_MS2Decal", "title": "Plot bargraph of oversampled 3D-peaks.", "topics": [ "plot_MS2Decal" ] }, { "page": "plot_MS2Oversampling", "title": "Plot bargraph of oversampled 3D-peaks.", "topics": [ "plot_MS2Oversampling" ] }, { "page": "plot_peptideMods", "title": "Plot peptide modification frequencies", "topics": [ "plot_peptideMods" ] }, { "page": "plot_RatiosPG", "title": "Plot ratios of labeled data (e.g. SILAC) from proteinGroups.txt", "topics": [ "plot_RatiosPG" ] }, { "page": "plot_RTPeakWidth", "title": "Plot RT peak width over time", "topics": [ "plot_RTPeakWidth" ] }, { "page": "plot_ScanIDRate", "title": "Plot line graph of TopN over Retention time.", "topics": [ "plot_ScanIDRate" ] }, { "page": "plot_TIC", "title": "Plot Total Ion Count over time", "topics": [ "plot_TIC" ] }, { "page": "plot_TopN", "title": "Plot line graph of TopN over Retention time.", "topics": [ "plot_TopN" ] }, { "page": "plot_TopNoverRT", "title": "Plot line graph of TopN over Retention time.", "topics": [ "plot_TopNoverRT" ] }, { "page": "plot_UncalibratedMSErr", "title": "A boxplot of uncalibrated mass errors for each Raw file.", "topics": [ "plot_UncalibratedMSErr" ] }, { "page": "plotTable", "title": "Plot a table with row names and title", "topics": [ "plotTable" ] }, { "page": "plotTableRaw", "title": "Colored table plot.", "topics": [ "plotTableRaw" ] }, { "page": "pointsPutX", "title": "Distribute a set of points with fixed y-values on a stretch of the x-axis.", "topics": [ "pointsPutX" ] }, { "page": "print.PTXQC_table", "title": "helper S3 class, enabling print(some-plot_Table-object)", "topics": [ "print.PTXQC_table" ] }, { "page": "printWithFooter", "title": "Augment a ggplot with footer text", "topics": [ "printWithFooter" ] }, { "page": "PTXQC", "title": "Quality control for proteomics data", "topics": [ "PTXQC" ] }, { "page": "QCMetaFilenames", "title": "Define a Singleton class which holds the full raw filenames (+path) and their PSI-MS CV terms for usage in the mzQC metadata", "topics": [ "QCMetaFilenames" ] }, { "page": "qcMetric_MSMSScans_TopNoverRT-class", "title": "Metric for msmsscans.txt, showing TopN over RT.", "topics": [ "qcMetric_MSMSScans_TopNoverRT", 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rmarkdown::render() instead of knitr::knit2html()'.", "Report Creation", "Q: A warning \"The file '<...>/mqpar.xml' was not found...\" in the console popped up.", "Report Interpretation", "Q: How do I know what the figures in the report mean?" ], "created": "2015-11-19 15:29:16", "modified": "2017-05-04 09:10:39", "commits": 9 }, { "source": "PTXQC-Input_And_Output_Data.Rmd", "filename": "PTXQC-Input_And_Output_Data.html", "title": "Input/Output data for PTXQC", "author": "Chris Bielow chris.bielow@fu-berlin.de", "engine": "knitr::rmarkdown", "headings": [ "Input/Output data for PTXQC", "Input", "Output" ], "created": "2015-11-01 14:32:21", "modified": "2026-04-23 13:34:42", "commits": 13 }, { "source": "PTXQC-ListOfMetrics.Rmd", "filename": "PTXQC-ListOfMetrics.html", "title": "List of Metrics", "author": "Chris Bielow chris.bielow@fu-berlin.de", "engine": "knitr::rmarkdown", "headings": [ "Overview ", "Metrics " ], "created": "2018-02-07 14:38:37", "modified": "2023-12-16 12:32:50", 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