PTXQC: Quality Report Generation for MaxQuant Results

Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the MaxQuant software suite (see <>). 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>.

AuthorChris Bielow <>
Date of publication2016-10-14 00:15:18
MaintainerChris Bielow <>

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Man pages

addGGtitle: Add title and subtitle to a ggplot

alignmentCheck: Verify an alignment by checking the retention time...

appendEnv: Add the value of a variable to an environment (fast append)

assignBlocks: Assign set numbers to a vector of values.

boxplotCompare: Boxplots - one for each condition (=column) in a data frame.

brewer.pal.Safe: Return color brew palettes, but fail hard if number of...

byX: Calls FUN on a subset of data in blocks of size 'subset_size'...

byXflex: Same as 'byX', but with more flexible group size, to avoid...

computeMatchRTFractions: Combine several data structs into a final picture for...

correctSetSize: Re-estimate a new set size to split a number of items into...

createReport: Create a quality control report (in PDF format).

CV: Coefficient of variation (CV)

del0: Replace 0 with NA in a vector

delLCP: Removes the longest common prefix (LCP) from a vector of...

delLCS: Removes the longest common suffix (LCS) from a vector of...

findAlignReference: Return list of raw file names which were reported by MaxQuant...

fixCalibration: Detect (and fix) MaxQuant mass recalibration columns, since...

flattenList: Flatten lists of lists with irregular depths to just a list...

getAbundanceClass: Assign a relative abundance class to a set of (log10)...

getECDF: Estimate the empirical density and return it

getFragmentErrors: Extract fragment mass deviation errors from a data.frame from...

getMaxima: Find the local maxima in a vector of numbers.

getMetaData: Extract meta information (orderNr, metric name, category)...

getMQPARValue: Retrieve a parameter value from a mqpar.xml file

getPCA: Create a principal component analysis (PCA) plot for the...

getPeptideCounts: Extract the number of peptides observed per Raw file from an...

getProteinCounts: Extract the number of protein groups observed per Raw file...

getQCHeatMap: Generate a Heatmap from a list of QC measurements.

getReportFilenames: Assembles a list of output file names, which will be created...

ggAxisLabels: Function to thin out the number of labels shown on an axis in...

ggText: Plot a text as graphic using ggplot2.

grapes-plus-grapes: A string concatenation function, more readable than...

grepv: Grep with values returned instead of indices.

idTransferCheck: Check how close transferred ID's after alignment are to their...

inMatchWindow: For grouped peaks: separate them into in-width vs. out-width...

lcpCount: Count the number of chars of the longest common prefix

LCS: Compute longest common substring of two strings.

lcsCount: Count the number of chars of the longest common suffix

LCSn: Find longest common substring from 'n' strings.

longestCommonPrefix: Get the longest common prefix from a set of strings.

longestCommonSuffix: Like longestCommonPrefix(), but on the suffix.

mosaicize: Prepare a Mosaic plot of two columns in long format.

MQDataReader-cash-getInvalidLines: Detect broken lines (e.g. due to Excel import+export)

MQDataReader-cash-getShortNames: Shorten a set of Raw file names and return a data frame with...

MQDataReader-cash-new: Constructor for class 'MQDataReader'.

MQDataReader-cash-plotNameMapping: Plots the current mapping of Raw file names to their...

MQDataReader-cash-readMappingFile: Reads a mapping table of full Raw file names to shortened...

MQDataReader-cash-readMQ: Wrapper to read a MQ txt file (e.g. proteinGroups.txt).

MQDataReader-cash-substitute: Replaces values in the member with (binary) values.

MQDataReader-cash-writeMappingFile: Writes a mapping table of full Raw file names to shortened...

pasten: paste with newline as separator

pastet: paste with tab as separator

peakSegmentation: Determine fraction of evidence which causes segmentation,...

peakWidthOverTime: Discretize RT peak widths by averaging values per time bin.

plot_CalibratedMSErr: Plot bargraph of uncalibrated mass errors for each Raw file.

plot_Charge: Plot MaxQuant Match-between-runs id transfer performance.

plot_ContEVD: Plot contaminants from evidence.txt, broken down into...

plot_ContsPG: Plot contaminants from proteinGroups.txt

plot_ContUser: Plot user-defined contaminants from evidence.txt

plot_ContUserScore: Plot Andromeda score distribution of contaminant peptide vs....

plot_CountData: Plot Protein groups per Raw file

plot_IDRate: Plot percent of identified MS/MS for each Raw file.

plot_IDsOverRT: Plot IDs over time for each Raw file.

plot_IonInjectionTimeOverRT: Plot line graph of TopN over Retention time.

plot_MBRAlign: Plot MaxQuant Match-between-runs alignment performance.

plot_MBRgain: Plot MaxQuant Match-between-runs id transfer performance.

plot_MBRIDtransfer: Plot MaxQuant Match-between-runs id transfer performance.

plot_MissedCleavages: Plot bargraph of missed cleavages.

plot_MS2Decal: Plot bargraph of oversampled 3D-peaks.

plot_MS2Oversampling: Plot bargraph of oversampled 3D-peaks.

plot_RatiosPG: Plot ratios of labeled data (e.g. SILAC) from...

plot_RTPeakWidth: Plot RT peak width over time

plot_ScanIDRate: Plot line graph of TopN over Retention time.

plotTable: Plot a table with row names and title

plotTableRaw: Colored table plot.

plot_TopN: Plot line graph of TopN over Retention time.

plot_TopNoverRT: Plot line graph of TopN over Retention time.

plot_UncalibratedMSErr: A boxplot of uncalibrated mass errors for each Raw file.

pointsPutX: Distribute a set of points with fixed y-values on a stretch...

print.PTXQC_table: helper S3 class, enabling print(some-plot_Table-object)

printWithFooter: Augment a ggplot with footer text

qcMetric-class: Class which can compute plots (usually for a single metric).

qcMetric_MSMSScans_TopNoverRT-class: Metric for msmsscans.txt, showing TopN over RT.

qualBestKS: From a list of vectors, compute all vs. all...

qualCentered: Quality metric for 'centeredness' of a distribution around...

qualCenteredRef: Quality metric for 'centeredness' of a distribution around...

qualGaussDev: Compute probability of Gaussian (mu=m, sd=s) at a position 0,...

qualHighest: Score an empirical density distribution of values, where the...

qualLinThresh: Quality metric with linear response to input, reaching the...

qualMedianDist: Quality metric which measures the absolute distance from...

qualUniform: Compute deviation from uniform distribution

read.MQ: Convenience wrapper for MQDataReader when only a single MQ...

renameFile: Given a vector of (short/long) filenames, translate to the...

repEach: Repeat each element x_i in X, n_i times.

RSD: Relative standard deviation (RSD)

RTalignmentTree: Return a tree plot with a possible alignment tree.

scale_x_discrete_reverse: Inverse the order of items on the x-axis (for discrete...

scale_y_discrete_reverse: Inverse the order of items on the y-axis (for discrete...

ScoreInAlignWindow: Compute the fraction of features per Raw file which have an...

shortenStrings: Shorten a string to a maximum length and indicate shorting by...

simplifyNames: Removes common substrings (infixes) in a set of strings.

supCount: Compute shortest prefix length which makes all strings in a...

theme_blank: A blank theme (similar to the deprecated theme_blank())

thinOut: Thin out a data.frame by removing rows with similar numerical...

thinOutBatch: Apply 'thinOut' on all subsets of a data.frame, split by a...

wait_for_writable: Check if a file is writable and blocks an interactive...

YAMLClass-class: Query a YAML object for a certain parameter.

Files in this package

PTXQC/R/MQDataReader.R PTXQC/R/fcn_misc.R PTXQC/R/fcn_MQalign.R PTXQC/R/qcMetric_PAR.R PTXQC/R/fcn_qualities.R PTXQC/R/fcn_PCA.R PTXQC/R/fcn_YAML.R PTXQC/R/qcMetric_PG.R PTXQC/R/qcMetric_MSMS.R PTXQC/R/fcn_computeQC.R PTXQC/R/fcn_miscGGplot.R PTXQC/R/fcn_MQ.R PTXQC/R/pkg_internal.R PTXQC/R/fcn_plots.R PTXQC/R/qcMetric_EVD.R PTXQC/R/qcMetric_MSMSScans.R PTXQC/R/qcMetric.R PTXQC/R/fcn_mqpar.R PTXQC/R/qcMetric_SM.R PTXQC/R/fcn_QCHeat.R
PTXQC/man/grepv.Rd PTXQC/man/longestCommonSuffix.Rd PTXQC/man/wait_for_writable.Rd PTXQC/man/RSD.Rd PTXQC/man/MQDataReader-cash-new.Rd PTXQC/man/plotTable.Rd PTXQC/man/MQDataReader-cash-substitute.Rd PTXQC/man/getProteinCounts.Rd PTXQC/man/peakWidthOverTime.Rd PTXQC/man/getPeptideCounts.Rd PTXQC/man/plot_IonInjectionTimeOverRT.Rd PTXQC/man/mosaicize.Rd PTXQC/man/qualBestKS.Rd PTXQC/man/plot_MS2Decal.Rd PTXQC/man/findAlignReference.Rd PTXQC/man/qualCentered.Rd PTXQC/man/plot_MBRgain.Rd PTXQC/man/printWithFooter.Rd PTXQC/man/plot_RTPeakWidth.Rd PTXQC/man/pasten.Rd PTXQC/man/getMQPARValue.Rd PTXQC/man/MQDataReader-cash-plotNameMapping.Rd PTXQC/man/plot_ContUserScore.Rd PTXQC/man/MQDataReader-cash-getShortNames.Rd PTXQC/man/thinOut.Rd PTXQC/man/lcsCount.Rd PTXQC/man/CV.Rd PTXQC/man/longestCommonPrefix.Rd PTXQC/man/plot_IDRate.Rd PTXQC/man/plot_RatiosPG.Rd PTXQC/man/ggText.Rd PTXQC/man/assignBlocks.Rd PTXQC/man/plot_ContEVD.Rd PTXQC/man/plot_TopNoverRT.Rd PTXQC/man/getMetaData.Rd PTXQC/man/plot_UncalibratedMSErr.Rd PTXQC/man/getPCA.Rd PTXQC/man/ggAxisLabels.Rd PTXQC/man/plot_CountData.Rd PTXQC/man/inMatchWindow.Rd PTXQC/man/plot_Charge.Rd PTXQC/man/plot_MBRIDtransfer.Rd PTXQC/man/pastet.Rd PTXQC/man/delLCP.Rd PTXQC/man/peakSegmentation.Rd PTXQC/man/computeMatchRTFractions.Rd PTXQC/man/MQDataReader-cash-readMQ.Rd PTXQC/man/qcMetric-class.Rd PTXQC/man/plot_CalibratedMSErr.Rd PTXQC/man/byX.Rd PTXQC/man/plot_ContsPG.Rd PTXQC/man/fixCalibration.Rd PTXQC/man/scale_y_discrete_reverse.Rd PTXQC/man/createReport.Rd PTXQC/man/getFragmentErrors.Rd PTXQC/man/print.PTXQC_table.Rd PTXQC/man/qualLinThresh.Rd PTXQC/man/getQCHeatMap.Rd PTXQC/man/plot_IDsOverRT.Rd PTXQC/man/plot_TopN.Rd PTXQC/man/MQDataReader-cash-getInvalidLines.Rd PTXQC/man/scale_x_discrete_reverse.Rd PTXQC/man/plot_MBRAlign.Rd PTXQC/man/plot_ScanIDRate.Rd PTXQC/man/simplifyNames.Rd PTXQC/man/boxplotCompare.Rd PTXQC/man/plot_ContUser.Rd PTXQC/man/del0.Rd PTXQC/man/LCSn.Rd PTXQC/man/theme_blank.Rd PTXQC/man/grapes-plus-grapes.Rd PTXQC/man/getECDF.Rd PTXQC/man/flattenList.Rd PTXQC/man/MQDataReader-cash-readMappingFile.Rd PTXQC/man/getMaxima.Rd PTXQC/man/shortenStrings.Rd PTXQC/man/getReportFilenames.Rd PTXQC/man/idTransferCheck.Rd PTXQC/man/supCount.Rd PTXQC/man/qualHighest.Rd PTXQC/man/qualUniform.Rd PTXQC/man/LCS.Rd PTXQC/man/thinOutBatch.Rd PTXQC/man/alignmentCheck.Rd PTXQC/man/byXflex.Rd PTXQC/man/addGGtitle.Rd PTXQC/man/YAMLClass-class.Rd PTXQC/man/qualMedianDist.Rd PTXQC/man/getAbundanceClass.Rd PTXQC/man/qcMetric_MSMSScans_TopNoverRT-class.Rd PTXQC/man/plot_MS2Oversampling.Rd PTXQC/man/ScoreInAlignWindow.Rd PTXQC/man/MQDataReader-cash-writeMappingFile.Rd PTXQC/man/plot_MissedCleavages.Rd PTXQC/man/repEach.Rd PTXQC/man/read.MQ.Rd PTXQC/man/plotTableRaw.Rd PTXQC/man/appendEnv.Rd PTXQC/man/RTalignmentTree.Rd PTXQC/man/renameFile.Rd PTXQC/man/qualCenteredRef.Rd PTXQC/man/delLCS.Rd PTXQC/man/brewer.pal.Safe.Rd PTXQC/man/correctSetSize.Rd PTXQC/man/qualGaussDev.Rd PTXQC/man/lcpCount.Rd PTXQC/man/pointsPutX.Rd

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