# An R package for quality Control for hydrogen deuterium exchange mass spectrometry experiments

## Documentation for package ‘hdxmsqc’ version 1.8.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

BRD4df | This is data to be included in my package
BRD4df_full | This is data to be included in my package
chargeCorrelationHdx | Charge states should have correlated incorperation but they need not be exactly the same
compatibleUptake | Check whether deuterium uptakes are compatible with difference overlapping sequences.
computeMassError | Empirical versus theoretical mass errors
computeMonotoneStats | Monotonicity based outlier detection.
exchangeableAmides | Compute exchangeable amides.
fourierIsotope | fourier transform approach to computing isotopic distribution
generateSpectra | generate Spectra using a fourier transform
hdxmsqc | A package to perfrom quality control for mass-spectrometry based hydrogen deuterium exchange experiment.
imTimeOutlier | Ion Mobility time based outlier analysis
intensityOutliers | Intensity based deviations
isMissingAtRandom | Missing at random versus missing not at random
isotopicDistributionHDXfourier | fourier transform approach to computing isotopic distribution
plotImTimeOutlier | Ion Mobility time based outlier analysis
plotIntensityOutliers | Intensity based deviation plot
plotMassError | Mass error plot
plotMissing | missing value plot
plotMonotoneStat | Monotonicity based outlier detection, plot.
plotrTimeOutliers | Retention time based analysis
processHDE | Function to curate and HDExaminer file so that in contains all the information in a sensible format. This object can then be straightforwardly passed to a object of class 'QFeatures'
qualityControl | Quality Control table function. Generate a table that collates quality control metrics
replicateCorrelation | Correlation based checks
replicateOutlier | Correlation based checks
rTimeOutliers | Retention time based analysis
spectraSimilarity | Spectral checking using data from HDsite