A B C D F G I L M P Q R S T W Y misc
addGGtitle | Add title and subtitle to a ggplot |
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) |
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). |
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). |
CV | Coefficient of variation (CV) |
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 |
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 |
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. |
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 |
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$getInvalidLines | Detect broken lines (e.g. due to Excel import+export) |
MQDataReader$getShortNames | Shorten a set of Raw file names and return a data frame with the mappings. |
MQDataReader$new | Constructor for class 'MQDataReader'. |
MQDataReader$plotNameMapping | Plots the current mapping of Raw file names to their shortened version. |
MQDataReader$readMappingFile | Reads a mapping table of full Raw file names to shortened names. |
MQDataReader$readMQ | Wrapper to read a MQ txt file (e.g. proteinGroups.txt). |
MQDataReader$substitute | Replaces values in the mq.data member with (binary) values. |
MQDataReader$writeMappingFile | Writes a mapping table of full Raw file names to shortened names. |
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_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_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 |
qcMetric | Class which can compute plots (usually for a single metric). |
qcMetric-class | Class which can compute plots (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. |
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. |
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. |
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. |
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()'. |