A B C D F G H I L M N P Q R S T W Y misc
| 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. |
| CV | Coefficient of variation (CV) |
| CVDictionarySingleton | Define a Singleton class which can hold a CV dictionary (so we do not have to load the .obo files over and over again) |
| 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. |
| 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). |
| fromDatatoMzQC | Allow conversion of plain named lists to mzQC objects |
| getAbundanceClass | Assign a relative abundance class to a set of (log10) abundance values |
| getCVDictionary | Parse the content of 'qc-cv.obo' and 'psi-ms.obo' from the 'PTXQC/cv/' folder and return their union as ontology |
| getCVTemplate | Fills a MzQCcvParameter object with id(accession) and name. The value (if any) needs to be set afterwards. |
| getECDF | Estimate the empirical density and return it |
| 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. |
| getQualityMetricTemplate | Fills a MzQCqualityMetric object with id(accession) and name. The value (if any) and unit (if any) need to be set afterwards. |
| 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. |
| hasFileSuffix | Checks if filepath ends in suffix. If suffix does not start with a '.' it is prepended automatically. |
| 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. |
| isUndefined | Tell if a string is undefined (NA or NULL); If yes, and its required by the mzQC standard, we can raise an error |
| isValidMzQC | Checks validity (= completeness) of mzQC objects - or lists (JSON arrays) thereof |
| 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 | S5-RefClass to read MaxQuant .txt files |
| MQDataReader-class | S5-RefClass to read MaxQuant .txt files |
| MzQCanalysisSoftware | Details of the software used to create the QC metrics |
| MzQCanalysisSoftware-class | Details of the software used to create the QC metrics |
| MzQCbaseQuality | Base class of runQuality/setQuality |
| MzQCbaseQuality-class | Base class of runQuality/setQuality |
| MzQCcontrolledVocabulary | An controlled vocabulary document, usually pointing to an .obo file |
| MzQCcontrolledVocabulary-class | An controlled vocabulary document, usually pointing to an .obo file |
| MzQCcvParameter | An controlled vocabulary parameter, as detailed in the OBO file |
| MzQCcvParameter-class | An controlled vocabulary parameter, as detailed in the OBO file |
| MzQCDateTime | An mzQC-formatted date+time, as required by the mzQC spec doc |
| MzQCDateTime-class | An mzQC-formatted date+time, as required by the mzQC spec doc |
| MzQCinputFile | An inputfile within metadata for a run/setQuality |
| MzQCinputFile-class | An inputfile within metadata for a run/setQuality |
| MzQCmetadata | The metadata for a run/setQuality |
| MzQCmetadata-class | The metadata for a run/setQuality |
| MzQCmzQC | Root element of an mzQC document |
| MzQCmzQC-class | Root element of an mzQC document |
| MzQCqualityMetric | The central class to store QC information |
| MzQCqualityMetric-class | The central class to store QC information |
| 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. |
| NULL_to_charNA | converts a NULL to NA_character_; or returns the argument unchanged otherwise |
| NULL_to_NA | converts a NULL to NA; or returns the argument unchanged otherwise |
| parseOBO | Get the information of each CV term from an obo file. |
| 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_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) |
| 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 |
| read.MQ | Convenience wrapper for MQDataReader when only a single MQ file should be read and file mapping need not be stored. |
| removeSuffix | Removes the last suffix (including the last dot) from a filename. If no dot exists, the full string is returned. |
| 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. |
| 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. |
| suffixToCV | For a given filename, check the suffix and translate it to an PSI-MS CV term, e.g. 'MS:1000584' |
| 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. |
| writeMZQC | Writes a full mzQC object to disk |
| YAMLClass | Query a YAML object for a certain parameter. |
| YAMLClass-class | Query a YAML object for a certain parameter. |
| %+% | A string concatenation function, more readable than 'paste()'. |