Man pages for PTXQC
Quality Report Generation for MaxQuant Results

addGGtitleAdd title and subtitle to a ggplot
alignmentCheckVerify an alignment by checking the retention time...
appendEnvAdd the value of a variable to an environment (fast append)
assignBlocksAssign set numbers to a vector of values.
boxplotCompareBoxplots - one for each condition (=column) in a data frame.
brewer.pal.SafeReturn color brew palettes, but fail hard if number of...
byXCalls FUN on a subset of data in blocks of size 'subset_size'...
byXflexSame as 'byX', but with more flexible group size, to avoid...
computeMatchRTFractionsCombine several data structs into a final picture for...
correctSetSizeRe-estimate a new set size to split a number of items into...
createReportCreate a quality control report (in PDF format).
CVCoefficient of variation (CV)
del0Replace 0 with NA in a vector
delLCPRemoves the longest common prefix (LCP) from a vector of...
delLCSRemoves the longest common suffix (LCS) from a vector of...
findAlignReferenceReturn list of raw file names which were reported by MaxQuant...
fixCalibrationDetect (and fix) MaxQuant mass recalibration columns, since...
flattenListFlatten lists of lists with irregular depths to just a list...
getAbundanceClassAssign a relative abundance class to a set of (log10)...
getECDFEstimate the empirical density and return it
getFragmentErrorsExtract fragment mass deviation errors from a data.frame from...
getHTMLTableCreate an HTML table with an extra header row
getMaximaFind the local maxima in a vector of numbers.
getMetaDataExtract meta information (orderNr, metric name, category)...
getMQPARValueRetrieve a parameter value from a mqpar.xml file
getPCACreate a principal component analysis (PCA) plot for the...
getPeptideCountsExtract the number of peptides observed per Raw file from an...
getProteinCountsExtract the number of protein groups observed per Raw file...
getQCHeatMapGenerate a Heatmap from a list of QC measurements.
getReportFilenamesAssembles a list of output file names, which will be created...
ggAxisLabelsFunction to thin out the number of labels shown on an axis in...
ggTextPlot a text as graphic using ggplot2.
grapes-plus-grapesA string concatenation function, more readable than...
grepvGrep with values returned instead of indices.
idTransferCheckCheck how close transferred ID's after alignment are to their...
inMatchWindowFor grouped peaks: separate them into in-width vs. out-width...
lcpCountCount the number of chars of the longest common prefix
LCSCompute longest common substring of two strings.
lcsCountCount the number of chars of the longest common suffix
LCSnFind longest common substring from 'n' strings.
longestCommonPrefixGet the longest common prefix from a set of strings.
longestCommonSuffixLike longestCommonPrefix(), but on the suffix.
mosaicizePrepare a Mosaic plot of two columns in long format.
MQDataReader-cash-getInvalidLinesDetect broken lines (e.g. due to Excel import+export)
MQDataReader-cash-getShortNamesShorten a set of Raw file names and return a data frame with...
MQDataReader-cash-newConstructor for class 'MQDataReader'.
MQDataReader-cash-plotNameMappingPlots the current mapping of Raw file names to their...
MQDataReader-cash-readMappingFileReads a mapping table of full Raw file names to shortened...
MQDataReader-cash-readMQWrapper to read a MQ txt file (e.g. proteinGroups.txt).
MQDataReader-cash-substituteReplaces values in the mq.data member with (binary) values.
MQDataReader-cash-writeMappingFileWrites a mapping table of full Raw file names to shortened...
pastenpaste with newline as separator
pastetpaste with tab as separator
peakSegmentationDetermine fraction of evidence which causes segmentation,...
peakWidthOverTimeDiscretize RT peak widths by averaging values per time bin.
plot_CalibratedMSErrPlot bargraph of uncalibrated mass errors for each Raw file.
plot_ChargeThe plots shows the charge distribution per Raw file. The...
plot_ContEVDPlot contaminants from evidence.txt, broken down into...
plot_ContsPGPlot contaminants from proteinGroups.txt
plot_ContUserPlot user-defined contaminants from evidence.txt
plot_ContUserScorePlot Andromeda score distribution of contaminant peptide vs....
plot_CountDataPlot Protein groups per Raw file
plot_IDRatePlot percent of identified MS/MS for each Raw file.
plot_IDsOverRTPlot IDs over time for each Raw file.
plot_IonInjectionTimeOverRTPlot line graph of TopN over Retention time.
plot_MBRAlignPlot MaxQuant Match-between-runs alignment performance.
plot_MBRgainPlot MaxQuant Match-between-runs id transfer performance.
plot_MBRIDtransferPlot MaxQuant Match-between-runs id transfer performance.
plot_MissedCleavagesPlot bargraph of missed cleavages.
plot_MS2DecalPlot bargraph of oversampled 3D-peaks.
plot_MS2OversamplingPlot bargraph of oversampled 3D-peaks.
plot_RatiosPGPlot ratios of labeled data (e.g. SILAC) from...
plot_RTPeakWidthPlot RT peak width over time
plot_ScanIDRatePlot line graph of TopN over Retention time.
plotTablePlot a table with row names and title
plotTableRawColored table plot.
plot_TopNPlot line graph of TopN over Retention time.
plot_TopNoverRTPlot line graph of TopN over Retention time.
plot_UncalibratedMSErrA boxplot of uncalibrated mass errors for each Raw file.
pointsPutXDistribute a set of points with fixed y-values on a stretch...
print.PTXQC_tablehelper S3 class, enabling print(some-plot_Table-object)
printWithFooterAugment a ggplot with footer text
qcMetric-classClass which can compute plots (usually for a single metric).
qcMetric_MSMSScans_TopNoverRT-classMetric for msmsscans.txt, showing TopN over RT.
qualBestKSFrom a list of vectors, compute all vs. all...
qualCenteredQuality metric for 'centeredness' of a distribution around...
qualCenteredRefQuality metric for 'centeredness' of a distribution around...
qualGaussDevCompute probability of Gaussian (mu=m, sd=s) at a position 0,...
qualHighestScore an empirical density distribution of values, where the...
qualLinThreshQuality metric with linear response to input, reaching the...
qualMedianDistQuality metric which measures the absolute distance from...
qualUniformCompute deviation from uniform distribution
read.MQConvenience wrapper for MQDataReader when only a single MQ...
renameFileGiven a vector of (short/long) filenames, translate to the...
repEachRepeat each element x_i in X, n_i times.
RSDRelative standard deviation (RSD)
RTalignmentTreeReturn a tree plot with a possible alignment tree.
scale_x_discrete_reverseInverse the order of items on the x-axis (for discrete...
scale_y_discrete_reverseInverse the order of items on the y-axis (for discrete...
ScoreInAlignWindowCompute the fraction of features per Raw file which have an...
shortenStringsShorten a string to a maximum length and indicate shorting by...
simplifyNamesRemoves common substrings (infixes) in a set of strings.
supCountCompute shortest prefix length which makes all strings in a...
theme_blankA blank theme (similar to the deprecated theme_blank())
thinOutThin out a data.frame by removing rows with similar numerical...
thinOutBatchApply 'thinOut' on all subsets of a data.frame, split by a...
wait_for_writableCheck if a file is writable and blocks an interactive...
YAMLClass-classQuery a YAML object for a certain parameter.
PTXQC documentation built on Nov. 17, 2017, 4:26 a.m.