| alignmentCheck | Verify an alignment by checking the retention time... |
| appendEnv | Add the value of a variable to an environment (fast append) |
| assembleMZQC | Collects all 'mzQC' members from each entry in lst_qcMetrics... |
| 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... |
| checkEnglishLocale | When MaxQuant is run with a wrong locale (i.e. the decimal... |
| 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). |
| createYaml | Creates a yaml file storing the parameters that are used for... |
| CV | Coefficient of variation (CV) |
| darken | Make a color (given as name or in RGB) darker by factor x =... |
| 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... |
| FilenameMapper-class | Make sure to call $readMappingFile(some_file) if you want to... |
| 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 |
| getFileEncoding | Determine if a file is 'UTF-8' or 'UTF-8-BOM' (as of MQ2.4)... |
| getFragmentErrors | Extract fragment mass deviation errors from a data.frame from... |
| 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)... |
| getMetaFilenames | Parses the given mqpar.xml file (or, if not found, tries the... |
| 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... |
| 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... |
| getRunQualityTemplate | Get an mzQC runQuality without actual metrics, but with full... |
| 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. |
| 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-class | S5-RefClass to read MaxQuant .txt files |
| MzTabReader-class | Class to read an mzTab file and store the tables internally. |
| 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 | The plots shows the charge distribution per Raw file. The... |
| 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_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 as a... |
| 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... |
| 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_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... |
| print.PTXQC_table | helper S3 class, enabling print(some-plot_Table-object) |
| printWithFooter | Augment a ggplot with footer text |
| PTXQC | Quality control for proteomics data |
| PTXQC-package | PTXQC: A package for computing Quality Control (QC) metrics... |
| QCMetaFilenames | Define a Singleton class which holds the full raw filenames... |
| qcMetric-class | Class which can compute plots and generate mzQC output... |
| 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. |
| scale01linear | Scales a vector of values linearly to [0, 1] If all input... |
| 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. |
