PTXQC: Quality Report Generation for MaxQuant Results

Share:

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

Author
Chris Bielow <chris.bielow@mdc-berlin.de>
Date of publication
2016-10-14 00:15:18
Maintainer
Chris Bielow <chris.bielow@mdc-berlin.de>
License
GPL-2
Version
0.80.14
URLs

View on CRAN

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 mq.data 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
PTXQC/inst
PTXQC/inst/examples
PTXQC/inst/examples/example_IDoverRT.png
PTXQC/inst/examples/report_v0.80.8__txt_5files_withMatch-100min.pdf
PTXQC/inst/examples/README.md
PTXQC/inst/examples/report_v0.80.8__txt_5files_withMatch-100min.html
PTXQC/inst/examples/example_heatmap.png
PTXQC/inst/examples/example_MBRalignment.png
PTXQC/inst/CITATION
PTXQC/inst/reportTemplate
PTXQC/inst/reportTemplate/PTXQC_report_template.Rmd
PTXQC/inst/doc
PTXQC/inst/doc/PTXQC-FAQ.html
PTXQC/inst/doc/PTXQC-Input_And_Output_Data.Rmd
PTXQC/inst/doc/PTXQC-Input_And_Output_Data.R
PTXQC/inst/doc/PTXQC-Input_And_Output_Data.html
PTXQC/inst/doc/PTXQC-Basic_Guide_for_R_users.Rmd
PTXQC/inst/doc/PTXQC-Basic_Guide_for_R_users.R
PTXQC/inst/doc/PTXQC-Basic_Guide_for_R_users.html
PTXQC/inst/doc/PTXQC-DragNDrop.Rmd
PTXQC/inst/doc/PTXQC-FAQ.Rmd
PTXQC/inst/doc/PTXQC-CustomizeReport.html
PTXQC/inst/doc/PTXQC-DragNDrop.html
PTXQC/inst/doc/PTXQC-CustomizeReport.Rmd
PTXQC/inst/dragNdrop
PTXQC/inst/dragNdrop/README.md
PTXQC/inst/dragNdrop/QC-dragdrop
PTXQC/inst/dragNdrop/QC-dragdrop/createQC_dragNdrop_withYAML.bat
PTXQC/inst/dragNdrop/QC-dragdrop/_internal
PTXQC/inst/dragNdrop/QC-dragdrop/_internal/compute_QC_report.R
PTXQC/inst/dragNdrop/QC-dragdrop/_internal/copy_complete_R_installation_folder_here.txt
PTXQC/inst/dragNdrop/QC-dragdrop/createQC_dragNdrop.bat
PTXQC/tests
PTXQC/tests/testthat.R
PTXQC/tests/testthat
PTXQC/tests/testthat/test_computeQC.R
PTXQC/tests/testthat/test_qualities.R
PTXQC/tests/testthat/test_misc.R
PTXQC/tests/testthat/test_qcMetric.R
PTXQC/NAMESPACE
PTXQC/NEWS
PTXQC/R
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/vignettes
PTXQC/vignettes/DragNDrop_Action.png
PTXQC/vignettes/PTXQC-Input_And_Output_Data.Rmd
PTXQC/vignettes/PTXQC-Basic_Guide_for_R_users.Rmd
PTXQC/vignettes/readme.txt
PTXQC/vignettes/DragNDrop_BatWindow.png
PTXQC/vignettes/PTXQC-DragNDrop.Rmd
PTXQC/vignettes/PTXQC-FAQ.Rmd
PTXQC/vignettes/PTXQC-CustomizeReport.Rmd
PTXQC/README.md
PTXQC/MD5
PTXQC/build
PTXQC/build/vignette.rds
PTXQC/DESCRIPTION
PTXQC/man
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