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

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Documentation for package ‘hdxmsqc’ version 1.1.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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