%+%                     A string concatenation function, more readable
                        than 'paste()'.
CV                      Coefficient of variation (CV)
FilenameMapper-class    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.
LCS                     Compute longest common substring of two
                        strings.
LCSn                    Find longest common substring from 'n' strings.
MQDataReader-class      S5-RefClass to read MaxQuant .txt files
MzTabReader-class       Class to read an mzTab file and store the
                        tables internally.
PTXQC                   Quality control for proteomics data
PTXQC-package           PTXQC: A package for computing Quality Control
                        (QC) metrics for Proteomics (PTX)
QCMetaFilenames         Define a Singleton class which holds the full
                        raw filenames (+path) and their PSI-MS CV terms
                        for usage in the mzQC metadata
RSD                     Relative standard deviation (RSD)
RTalignmentTree         Return a tree plot with a possible alignment
                        tree.
ScoreInAlignWindow      Compute the fraction of features per Raw file
                        which have an acceptable RT difference after
                        alignment
YAMLClass-class         Query a YAML object for a certain parameter.
alignmentCheck          Verify an alignment by checking the retention
                        time differences of identical peptides across
                        Raw files
appendEnv               Add the value of a variable to an environment
                        (fast append)
assembleMZQC            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
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 requested colors is larger than the
                        palette is holding.
byX                     Calls FUN on a subset of data in blocks of size
                        'subset_size' of unique indices.
byXflex                 Same as 'byX', but with more flexible group
                        size, to avoid that the last group has only a
                        few entries (<50% of desired size).
checkEnglishLocale      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
computeMatchRTFractions
                        Combine several data structs into a final
                        picture for segmentation incurred by
                        'Match-between-runs'.
correctSetSize          Re-estimate a new set size to split a number of
                        items into equally sized sets.
createReport            Create a quality control report (in PDF
                        format).
createYaml              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.
darken                  Make a color (given as name or in RGB) darker
                        by factor x = [0 = black, 1=unchanged]
del0                    Replace 0 with NA in a vector
delLCP                  Removes the longest common prefix (LCP) from a
                        vector of strings.
delLCS                  Removes the longest common suffix (LCS) from a
                        vector of strings.
findAlignReference      Return list of raw file names which were
                        reported by MaxQuant as reference point for
                        alignment.
fixCalibration          Detect (and fix) MaxQuant mass recalibration
                        columns, since they sometimes report wrong
                        values.
flattenList             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).
getAbundanceClass       Assign a relative abundance class to a set of
                        (log10) abundance values
getECDF                 Estimate the empirical density and return it
getFileEncoding         Determine if a file is 'UTF-8' or 'UTF-8-BOM'
                        (as of MQ2.4) or 'UTF-16BE' or 'UTF-16LE'
getFragmentErrors       Extract fragment mass deviation errors from a
                        data.frame from msms.txt
getHTMLTable            Create an HTML table with an extra header row
getMQPARValue           Retrieve a parameter value from a mqpar.xml
                        file
getMaxima               Find the local maxima in a vector of numbers.
getMetaData             Extract meta information (orderNr, metric name,
                        category) from a list of Qc metric objects
getMetaFilenames        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
getMetricsObjects       Get all currently available metrics
getPCA                  Create a principal component analysis (PCA)
                        plot for the first two dimensions.
getPeptideCounts        Extract the number of peptides observed per Raw
                        file from an evidence table.
getProteinCounts        Extract the number of protein groups observed
                        per Raw file from an evidence table.
getQCHeatMap            Generate a Heatmap from a list of QC
                        measurements.
getReportFilenames      Assembles a list of output file names, which
                        will be created during reporting.
getRunQualityTemplate   Get an mzQC runQuality without actual metrics,
                        but with full metadata
ggAxisLabels            Function to thin out the number of labels shown
                        on an axis in GGplot
ggText                  Plot a text as graphic using ggplot2.
grepv                   Grep with values returned instead of indices.
idTransferCheck         Check how close transferred ID's after
                        alignment are to their genuine IDs within one
                        Raw file.
inMatchWindow           For grouped peaks: separate them into in-width
                        vs. out-width class.
lcpCount                Count the number of chars of the longest common
                        prefix
lcsCount                Count the number of chars of the longest common
                        suffix
longestCommonPrefix     Get the longest common prefix from a set of
                        strings.
longestCommonSuffix     Like longestCommonPrefix(), but on the suffix.
modsToTable             Convert list of (mixed)modifications to a
                        frequency table
modsToTableByRaw        Convert list of (mixed)modifications to a
                        frequency table
mosaicize               Prepare a Mosaic plot of two columns in long
                        format.
pasten                  paste with newline as separator
pastet                  paste with tab as separator
peakSegmentation        Determine fraction of evidence which causes
                        segmentation, i.e. sibling peaks at different
                        RTs confirmed either by genuine or transferred
                        MS/MS.
peakWidthOverTime       Discretize RT peak widths by averaging values
                        per time bin.
plotTable               Plot a table with row names and title
plotTableRaw            Colored table plot.
plot_CalibratedMSErr    Plot bargraph of uncalibrated mass errors for
                        each Raw file.
plot_Charge             The plots shows the charge distribution per Raw
                        file. The output of 'mosaicize()' can be used
                        directly.
plot_ContEVD            Plot contaminants from evidence.txt, broken
                        down into top5-proteins.
plot_ContUser           Plot user-defined contaminants from
                        evidence.txt
plot_ContUserScore      Plot Andromeda score distribution of
                        contaminant peptide vs. matrix peptides.
plot_ContsPG            Plot contaminants from proteinGroups.txt
plot_CountData          Plot Protein groups per Raw file
plot_DataOverRT         Plot some count data over time for each 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_MBRIDtransfer      Plot MaxQuant Match-between-runs id transfer
                        performance.
plot_MBRgain            Plot MaxQuant Match-between-runs id transfer
                        performance as a scatterplot.
plot_MS2Decal           Plot bargraph of oversampled 3D-peaks.
plot_MS2Oversampling    Plot bargraph of oversampled 3D-peaks.
plot_MissedCleavages    Plot bargraph of missed cleavages.
plot_RTPeakWidth        Plot RT peak width over time
plot_RatiosPG           Plot ratios of labeled data (e.g. SILAC) from
                        proteinGroups.txt
plot_ScanIDRate         Plot line graph of TopN over Retention time.
plot_TIC                Plot Total Ion Count over time
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.
plot_peptideMods        Plot peptide modification frequencies
pointsPutX              Distribute a set of points with fixed y-values
                        on a stretch of the x-axis.
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 and generate mzQC
                        output (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
                        Kolmogorov-Smirnoff distance statistics (D)
qualCentered            Quality metric for 'centeredness' of a
                        distribution around zero.
qualCenteredRef         Quality metric for 'centeredness' of a
                        distribution around zero with a user-supplied
                        range threshold.
qualGaussDev            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.
qualHighest             Score an empirical density distribution of
                        values, where the best possible distribution is
                        right-skewed.
qualLinThresh           Quality metric with linear response to input,
                        reaching the maximum score at the given
                        threshold.
qualMedianDist          Quality metric which measures the absolute
                        distance from median.
qualUniform             Compute deviation from uniform distribution
read.MQ                 Convenience wrapper for MQDataReader when only
                        a single MQ file should be read and file
                        mapping need not be stored.
renameFile              Given a vector of (short/long) filenames,
                        translate to the (long/short) version
repEach                 Repeat each element x_i in X, n_i times.
scale01linear           Scales a vector of values linearly to [0, 1] If
                        all input values are equal, returned values are
                        all 0
scale_x_discrete_reverse
                        Inverse the order of items on the x-axis (for
                        discrete scales)
scale_y_discrete_reverse
                        Inverse the order of items on the y-axis (for
                        discrete scales)
shortenStrings          Shorten a string to a maximum length and
                        indicate shorting by appending '..'
simplifyNames           Removes common substrings (infixes) in a set of
                        strings.
supCount                Compute shortest prefix length which makes all
                        strings in a vector uniquely identifyable.
theme_blank             A blank theme (similar to the deprecated
                        theme_blank())
thinOut                 Thin out a data.frame by removing rows with
                        similar numerical values in a certain column.
thinOutBatch            Apply 'thinOut' on all subsets of a data.frame,
                        split by a batch column
wait_for_writable       Check if a file is writable and blocks an
                        interactive session, waiting for user input.
