Package: PTXQC 1.1.1

Chris Bielow

PTXQC: Quality Report Generation for MaxQuant and mzTab Results

Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the MaxQuant software suite (from .txt files) or mzTab files (ideally from OpenMS 'QualityControl' tool). Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format. Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015) <doi:10.1021/acs.jproteome.5b00780>.

Authors:Chris Bielow [aut, cre], Juliane Schmachtenberg [ctb], Swenja Wagner [ctb], Patricia Scheil [ctb], Tom Waschischek [ctb], Guido Mastrobuoni [dtc, rev]

PTXQC_1.1.1.tar.gz
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PTXQC.pdf |PTXQC.html✨
PTXQC/json (API)
NEWS

# Install 'PTXQC' in R:
install.packages('PTXQC', repos = c('https://cbielow.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/cbielow/ptxqc/issues

On CRAN:

drag-and-drophacktoberfestheatmapmatch-between-runsmaxquantmetricmztabopenmsproteomicsquality-controlquality-metricsreport

9.29 score 42 stars 1 packages 105 scripts 800 downloads 7 mentions 77 exports 96 dependencies

Last updated 11 months agofrom:41ea336a44. Checks:8 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 05 2025
R-4.5-winOKFeb 05 2025
R-4.5-macOKFeb 05 2025
R-4.5-linuxOKFeb 05 2025
R-4.4-winOKFeb 05 2025
R-4.4-macOKFeb 05 2025
R-4.3-winOKFeb 05 2025
R-4.3-macOKFeb 05 2025

Exports:assembleMZQCassignBlocksboxplotComparebyXbyXflexcorrectSetSizecreateReportcreateYamldelLCPdelLCSFilenameMappergetECDFgetFragmentErrorsgetHTMLTablegetMaximagetMQPARValuegetPCAgetReportFilenamesgrepvlcpCountLCSlcsCountLCSnlongestCommonPrefixlongestCommonSuffixmodsToTablemodsToTableByRawmosaicizepastenpastetpeakWidthOverTimeplot_CalibratedMSErrplot_Chargeplot_ContEVDplot_ContsPGplot_ContUserplot_ContUserScoreplot_CountDataplot_DataOverRTplot_IDRateplot_IDsOverRTplot_IonInjectionTimeOverRTplot_MBRAlignplot_MBRgainplot_MBRIDtransferplot_MissedCleavagesplot_MS2Decalplot_MS2Oversamplingplot_peptideModsplot_RatiosPGplot_RTPeakWidthplot_ScanIDRateplot_TICplot_TopNplot_TopNoverRTplot_UncalibratedMSErrplotTablepointsPutXQCMetaFilenamesqcMetricqualBestKSqualCenteredqualCenteredRefqualGaussDevqualHighestqualLinThreshqualMedianDistqualUniformread.MQrenameFilerepEachRTalignmentTreeshortenStringssimplifyNamessupCounttheme_blankYAMLClass

Dependencies:ade4backportsbase64encbriobslibcachemcallrcheckmateclicollectionscolorspacecpp11crayoncurldata.tabledescdiffobjdigestdplyrevaluatefansifarverfastmapfontawesomefsgenericsggdendroggplot2gluegridExtragtablehighrhtmlTablehtmltoolshtmlwidgetsisobandjquerylibjsonlitejsonvalidateknitrlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeontologyIndexpillarpixmappkgbuildpkgconfigpkgloadplyrpraiseprocessxpspurrrR6R6PrappdirsRColorBrewerRcppRcppArmadilloreshape2rlangrmarkdownrmzqcrprojrootrstudioapisassscalessegmentedseqinrspstringistringrtestthattibbletidyrtidyselecttinytexUpSetRutf8V8vctrsviridisLitewaldowithrxfunxml2yaml

Basic R-Usage Guide for PTXQC

Chris Bielow [email protected]

Rendered fromPTXQC-Basic_Guide_for_R_users.Rmdusingknitr::rmarkdownon Feb 05 2025.

Last update: 2020-01-16
Started: 2015-10-20

Customizing PTXQC reports

Chris Bielow [email protected]

Rendered fromPTXQC-CustomizeReport.Rmdusingknitr::rmarkdownon Feb 05 2025.

Last update: 2020-11-11
Started: 2015-10-20

Drag'n'drop Usage Guide for PTXQC

Chris Bielow [email protected]

Rendered fromPTXQC-DragNDrop.Rmdusingknitr::rmarkdownon Feb 05 2025.

Last update: 2017-04-03
Started: 2015-10-20

Frequently asked questions for PTXQC

Chris Bielow [email protected]

Rendered fromPTXQC-FAQ.Rmdusingknitr::rmarkdownon Feb 05 2025.

Last update: 2017-05-04
Started: 2015-11-19

Input/Output data for PTXQC

Chris Bielow [email protected]

Rendered fromPTXQC-Input_And_Output_Data.Rmdusingknitr::rmarkdownon Feb 05 2025.

Last update: 2023-05-17
Started: 2015-11-01

List of Metrics

Chris Bielow [email protected]

Rendered fromPTXQC-ListOfMetrics.Rmdusingknitr::rmarkdownon Feb 05 2025.

Last update: 2023-12-16
Started: 2018-02-07

Readme and manuals

Help Manual

Help pageTopics
PTXQC: A package for computing Quality Control (QC) metrics for Proteomics (PTX)PTXQC-package PTXQC
A string concatenation function, more readable than 'paste()'.%+%
Verify an alignment by checking the retention time differences of identical peptides across Raw filesalignmentCheck
Add the value of a variable to an environment (fast append)appendEnv
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 otherwiseassembleMZQC
Assign set numbers to a vector of values.assignBlocks
Boxplots - one for each condition (=column) in a data frame.boxplotCompare
Return color brew palettes, but fail hard if number of requested colors is larger than the palette is holding.brewer.pal.Safe
Calls FUN on a subset of data in blocks of size 'subset_size' of unique indices.byX
Same as 'byX', but with more flexible group size, to avoid that the last group has only a few entries (<50% of desired size).byXflex
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 annotationcheckEnglishLocale
Combine several data structs into a final picture for segmentation incurred by 'Match-between-runs'.computeMatchRTFractions
Re-estimate a new set size to split a number of items into equally sized sets.correctSetSize
Create a quality control report (in PDF format).createReport
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.createYaml
Coefficient of variation (CV)CV
Make a color (given as name or in RGB) darker by factor x = [0 = black, 1=unchanged]darken
Replace 0 with NA in a vectordel0
Removes the longest common prefix (LCP) from a vector of strings.delLCP
Removes the longest common suffix (LCS) from a vector of strings.delLCS
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.FilenameMapper FilenameMapper-class
Return list of raw file names which were reported by MaxQuant as reference point for alignment.findAlignReference
Detect (and fix) MaxQuant mass recalibration columns, since they sometimes report wrong values.fixCalibration
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).flattenList
Assign a relative abundance class to a set of (log10) abundance valuesgetAbundanceClass
Estimate the empirical density and return itgetECDF
Determine if a file is 'UTF-8' or 'UTF-8-BOM' (as of MQ2.4) or 'UTF-16BE' or 'UTF-16LE'getFileEncoding
Extract fragment mass deviation errors from a data.frame from msms.txtgetFragmentErrors
Create an HTML table with an extra header rowgetHTMLTable
Find the local maxima in a vector of numbers.getMaxima
Extract meta information (orderNr, metric name, category) from a list of Qc metric objectsgetMetaData
Get all currently available metricsgetMetricsObjects
Retrieve a parameter value from a mqpar.xml filegetMQPARValue
Create a principal component analysis (PCA) plot for the first two dimensions.getPCA
Extract the number of peptides observed per Raw file from an evidence table.getPeptideCounts
Extract the number of protein groups observed per Raw file from an evidence table.getProteinCounts
Generate a Heatmap from a list of QC measurements.getQCHeatMap
Assembles a list of output file names, which will be created during reporting.getReportFilenames
Get an mzQC runQuality without actual metrics, but with full metadatagetRunQualityTemplate
Function to thin out the number of labels shown on an axis in GGplotggAxisLabels
Plot a text as graphic using ggplot2.ggText
Grep with values returned instead of indices.grepv
Check how close transferred ID's after alignment are to their genuine IDs within one Raw file.idTransferCheck
For grouped peaks: separate them into in-width vs. out-width class.inMatchWindow
Count the number of chars of the longest common prefixlcpCount
Compute longest common substring of two strings.LCS
Count the number of chars of the longest common suffixlcsCount
Find longest common substring from 'n' strings.LCSn
Get the longest common prefix from a set of strings.longestCommonPrefix
Like longestCommonPrefix(), but on the suffix.longestCommonSuffix
Convert list of (mixed)modifications to a frequency tablemodsToTable
Convert list of (mixed)modifications to a frequency tablemodsToTableByRaw
Prepare a Mosaic plot of two columns in long format.mosaicize
S5-RefClass to read MaxQuant .txt filesMQDataReader MQDataReader-class
Class to read an mzTab file and store the tables internally.MzTabReader MzTabReader-class
paste with newline as separatorpasten
paste with tab as separatorpastet
Determine fraction of evidence which causes segmentation, i.e. sibling peaks at different RTs confirmed either by genuine or transferred MS/MS.peakSegmentation
Discretize RT peak widths by averaging values per time bin.peakWidthOverTime
Plot bargraph of uncalibrated mass errors for each Raw file.plot_CalibratedMSErr
The plots shows the charge distribution per Raw file. The output of 'mosaicize()' can be used directly.plot_Charge
Plot contaminants from evidence.txt, broken down into top5-proteins.plot_ContEVD
Plot contaminants from proteinGroups.txtplot_ContsPG
Plot user-defined contaminants from evidence.txtplot_ContUser
Plot Andromeda score distribution of contaminant peptide vs. matrix peptides.plot_ContUserScore
Plot Protein groups per Raw fileplot_CountData
Plot some count data over time for each Raw file.plot_DataOverRT
Plot percent of identified MS/MS for each Raw file.plot_IDRate
Plot IDs over time for each Raw file.plot_IDsOverRT
Plot line graph of TopN over Retention time.plot_IonInjectionTimeOverRT
Plot MaxQuant Match-between-runs alignment performance.plot_MBRAlign
Plot MaxQuant Match-between-runs id transfer performance.plot_MBRgain
Plot MaxQuant Match-between-runs id transfer performance.plot_MBRIDtransfer
Plot bargraph of missed cleavages.plot_MissedCleavages
Plot bargraph of oversampled 3D-peaks.plot_MS2Decal
Plot bargraph of oversampled 3D-peaks.plot_MS2Oversampling
Plot peptide modification frequenciesplot_peptideMods
Plot ratios of labeled data (e.g. SILAC) from proteinGroups.txtplot_RatiosPG
Plot RT peak width over timeplot_RTPeakWidth
Plot line graph of TopN over Retention time.plot_ScanIDRate
Plot Total Ion Count over timeplot_TIC
Plot line graph of TopN over Retention time.plot_TopN
Plot line graph of TopN over Retention time.plot_TopNoverRT
A boxplot of uncalibrated mass errors for each Raw file.plot_UncalibratedMSErr
Plot a table with row names and titleplotTable
Colored table plot.plotTableRaw
Distribute a set of points with fixed y-values on a stretch of the x-axis.pointsPutX
helper S3 class, enabling print(some-plot_Table-object)print.PTXQC_table
Augment a ggplot with footer textprintWithFooter
Define a Singleton class which holds the full raw filenames (+path) and their PSI-MS CV terms for usage in the mzQC metadataQCMetaFilenames
Metric for msmsscans.txt, showing TopN over RT.qcMetric_MSMSScans_TopNoverRT qcMetric_MSMSScans_TopNoverRT-class
Class which can compute plots and generate mzQC output (usually for a single metric).qcMetric qcMetric-class
From a list of vectors, compute all vs. all Kolmogorov-Smirnoff distance statistics (D)qualBestKS
Quality metric for 'centeredness' of a distribution around zero.qualCentered
Quality metric for 'centeredness' of a distribution around zero with a user-supplied range threshold.qualCenteredRef
Compute probability of Gaussian (mu=m, sd=s) at a position 0, with reference to the max obtainable probability of that Gaussian at its center.qualGaussDev
Score an empirical density distribution of values, where the best possible distribution is right-skewed.qualHighest
Quality metric with linear response to input, reaching the maximum score at the given threshold.qualLinThresh
Quality metric which measures the absolute distance from median.qualMedianDist
Compute deviation from uniform distributionqualUniform
Convenience wrapper for MQDataReader when only a single MQ file should be read and file mapping need not be stored.read.MQ
Given a vector of (short/long) filenames, translate to the (long/short) versionrenameFile
Repeat each element x_i in X, n_i times.repEach
Relative standard deviation (RSD)RSD
Return a tree plot with a possible alignment tree.RTalignmentTree
Inverse the order of items on the x-axis (for discrete scales)scale_x_discrete_reverse
Inverse the order of items on the y-axis (for discrete scales)scale_y_discrete_reverse
Scales a vector of values linearly to [0, 1] If all input values are equal, returned values are all 0scale01linear
Compute the fraction of features per Raw file which have an acceptable RT difference after alignmentScoreInAlignWindow
Shorten a string to a maximum length and indicate shorting by appending '..'shortenStrings
Removes common substrings (infixes) in a set of strings.simplifyNames
Compute shortest prefix length which makes all strings in a vector uniquely identifyable.supCount
A blank theme (similar to the deprecated theme_blank())theme_blank
Thin out a data.frame by removing rows with similar numerical values in a certain column.thinOut
Apply 'thinOut' on all subsets of a data.frame, split by a batch columnthinOutBatch
Check if a file is writable and blocks an interactive session, waiting for user input.wait_for_writable
Query a YAML object for a certain parameter.YAMLClass YAMLClass-class