Quality Report Generation for MaxQuant and mzTab Results

Documentation for package ‘PTXQC’ version 1.1.1

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PTXQC: A package for computing Quality Control (QC) metrics for Proteomics (PTX)

-- A --

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.

-- B --

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).

-- C --

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.
CV	Coefficient of variation (CV)

-- D --

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.

-- F --

FilenameMapper	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-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.
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).

-- G --

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
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
getMetricsObjects	Get all currently available metrics
getMQPARValue	Retrieve a parameter value from a mqpar.xml file
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.

-- I --

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.

-- L --

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.

-- M --

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.
MQDataReader	S5-RefClass to read MaxQuant .txt files
MQDataReader-class	S5-RefClass to read MaxQuant .txt files
MzTabReader	Class to read an mzTab file and store the tables internally.
MzTabReader-class	Class to read an mzTab file and store the tables internally.

-- P --

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_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. matrix peptides.
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_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_peptideMods	Plot peptide modification frequencies
plot_RatiosPG	Plot ratios of labeled data (e.g. SILAC) from proteinGroups.txt
plot_RTPeakWidth	Plot RT peak width over time
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.
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
PTXQC	PTXQC: A package for computing Quality Control (QC) metrics for Proteomics (PTX)

-- Q --

QCMetaFilenames	Define a Singleton class which holds the full raw filenames (+path) and their PSI-MS CV terms for usage in the mzQC metadata
qcMetric	Class which can compute plots and generate mzQC output (usually for a single metric).
qcMetric-class	Class which can compute plots and generate mzQC output (usually for a single metric).
qcMetric_MSMSScans_TopNoverRT	Metric for msmsscans.txt, showing TopN over RT.
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

-- R --

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.
RSD	Relative standard deviation (RSD)
RTalignmentTree	Return a tree plot with a possible alignment tree.

-- S --

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)
ScoreInAlignWindow	Compute the fraction of features per Raw file which have an acceptable RT difference after alignment
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.

-- T --

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

-- W --

wait_for_writable

Check if a file is writable and blocks an interactive session, waiting for user input.

-- Y --

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

-- misc --

%+%	A string concatenation function, more readable than 'paste()'.