Quality Report Generation for MaxQuant and mzTab Results
Get an mzQC runQuality without actual metrics, but with full metadata
Plot line graph of TopN over Retention time.
Plot Total Ion Count over time
Plot line graph of TopN over Retention time.
Plot line graph of TopN over Retention time.
Quality metric for 'centeredness' of a distribution around zero with a...
Compute probability of Gaussian (mu=m, sd=s) at a position 0, with ref...
Score an empirical density distribution of values, where the best poss...
Quality metric with linear response to input, reaching the maximum sco...
Quality metric which measures the absolute distance from median.
Compute deviation from uniform distribution
Convenience wrapper for MQDataReader when only a single MQ file should...
Given a vector of (short/long) filenames, translate to the (long/short...
Repeat each element x_i in X, n_i times.
Relative standard deviation (RSD)
Return a tree plot with a possible alignment tree.
Inverse the order of items on the x-axis (for discrete scales)
Inverse the order of items on the y-axis (for discrete scales)
Scales a vector of values linearly to [0, 1] If all input values are e...
Compute the fraction of features per Raw file which have an acceptable...
A boxplot of uncalibrated mass errors for each Raw file.
Plot a table with row names and title
Colored table plot.
Distribute a set of points with fixed y-values on a stretch of the x-a...
helper S3 class, enabling print(some-plot_Table-object)
Augment a ggplot with footer text
Shorten a string to a maximum length and indicate shorting by appendin...
Removes common substrings (infixes) in a set of strings.
Compute shortest prefix length which makes all strings in a vector uni...
A blank theme (similar to the deprecated theme_blank())
Thin out a data.frame by removing rows with similar numerical values i...
Apply 'thinOut' on all subsets of a data.frame, split by a batch colum...
Check if a file is writable and blocks an interactive session, waiting...
Query a YAML object for a certain parameter.
PTXQC: A package for computing Quality Control (QC) metrics for Proteo...
Define a Singleton class which holds the full raw filenames (+path) an...
Function to thin out the number of labels shown on an axis in GGplot
Plot a text as graphic using ggplot2.
A string concatenation function, more readable than 'paste()'.
Grep with values returned instead of indices.
Verify an alignment by checking the retention time differences of iden...
Add the value of a variable to an environment (fast append)
Collects all 'mzQC' members from each entry in lst_qcMetrics and store...
Assign set numbers to a vector of values.
Boxplots - one for each condition (=column) in a data frame.
Return color brew palettes, but fail hard if number of requested color...
Calls FUN on a subset of data in blocks of size 'subset_size' of uniqu...
Same as byX, but with more flexible group size, to avoid that the la...
When MaxQuant is run with a wrong locale (i.e. the decimal separator i...
Combine several data structs into a final picture for segmentation inc...
Class which can compute plots and generate mzQC output (usually for a ...
Re-estimate a new set size to split a number of items into equally siz...
Create a quality control report (in PDF format).
Creates a yaml file storing the parameters that are used for creating ...
Coefficient of variation (CV)
Make a color (given as name or in RGB) darker by factor x = [0 = black...
Replace 0 with NA in a vector
Metric for msmsscans.txt, showing TopN over RT.
Removes the longest common prefix (LCP) from a vector of strings.
Removes the longest common suffix (LCS) from a vector of strings.
Make sure to call $readMappingFile(some_file) if you want to support a...
Return list of raw file names which were reported by MaxQuant as refer...
Detect (and fix) MaxQuant mass recalibration columns, since they somet...
Flatten lists of lists with irregular depths to just a list of items, ...
Assign a relative abundance class to a set of (log10) abundance values
Estimate the empirical density and return it
Determine if a file is 'UTF-8' or 'UTF-8-BOM' (as of MQ2.4) or 'UTF-16...
Extract fragment mass deviation errors from a data.frame from msms.txt
Create an HTML table with an extra header row
Find the local maxima in a vector of numbers.
Extract meta information (orderNr, metric name, category) from a list ...
Get all currently available metrics
From a list of vectors, compute all vs. all Kolmogorov-Smirnoff distan...
Retrieve a parameter value from a mqpar.xml file
Create a principal component analysis (PCA) plot for the first two dim...
Extract the number of peptides observed per Raw file from an evidence ...
Extract the number of protein groups observed per Raw file from an evi...
Generate a Heatmap from a list of QC measurements.
Assembles a list of output file names, which will be created during re...
Check how close transferred ID's after alignment are to their genuine ...
For grouped peaks: separate them into in-width vs. out-width class.
Count the number of chars of the longest common prefix
Compute longest common substring of two strings.
Count the number of chars of the longest common suffix
Find longest common substring from 'n' strings.
Get the longest common prefix from a set of strings.
Like longestCommonPrefix(), but on the suffix.
Convert list of (mixed)modifications to a frequency table
Convert list of (mixed)modifications to a frequency table
Prepare a Mosaic plot of two columns in long format.
S5-RefClass to read MaxQuant .txt files
Quality metric for 'centeredness' of a distribution around zero.
Class to read an mzTab file and store the tables internally.
paste with newline as separator
paste with tab as separator
Determine fraction of evidence which causes segmentation, i.e. sibling...
Discretize RT peak widths by averaging values per time bin.
Plot bargraph of uncalibrated mass errors for each Raw file.
The plots shows the charge distribution per Raw file. The output of 'm...
Plot contaminants from evidence.txt, broken down into top5-proteins.
Plot contaminants from proteinGroups.txt
Plot user-defined contaminants from evidence.txt
Plot Andromeda score distribution of contaminant peptide vs. matrix pe...
Plot Protein groups per Raw file
Plot some count data over time for each Raw file.
Plot percent of identified MS/MS for each Raw file.
Plot IDs over time for each Raw file.
Plot line graph of TopN over Retention time.
Plot MaxQuant Match-between-runs alignment performance.
Plot MaxQuant Match-between-runs id transfer performance.
Plot MaxQuant Match-between-runs id transfer performance.
Plot bargraph of missed cleavages.
Plot bargraph of oversampled 3D-peaks.
Plot bargraph of oversampled 3D-peaks.
Plot peptide modification frequencies
Plot ratios of labeled data (e.g. SILAC) from proteinGroups.txt
Plot RT peak width over time
Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the MaxQuant software suite (from .txt files) or mzTab files (ideally from OpenMS 'QualityControl' tool). Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format. Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015) <doi:10.1021/acs.jproteome.5b00780>.