CMSproc-class: A class to hold chromatography-mass spectrometry...
In hansenlab/yamss: Tools for high-throughput metabolomics

Description Slots Utility functions Accessors Examples

This class builds on the CMSraw class to additionally store background-corrected intensities as well as the bivariate kernel density estimate.

colData:: a DataFrame of phenotype and sample information.
rawDT:: a data.table of raw spectral information.
mzParams:: a list containing the minimum and maximum M/Z value and number of scans in each sample.
rtAlign:: a logical indicating whether the data has been retention time aligned or not.
bgcorrDT:: a data.table of background-corrected spectral information.
density:: a matrix with rows corresponding to M/Z values and columns corresponding to scans containing the kernel density estimate.
densityQuantiles:: a numeric vector containing the 100 percent quantiles of the nonzero density values.

We have the following utility functions:

show:: The show method; prints the object.
getEICS:: Gets extracted ion chromatograms (EICs) for the supplied M/Z ranges.
plotDensityRegion:: Makes an image plot of the density estimate in a specified M/Z and scan region.

We have the following accessor functions:

colData:: Gets the DataFrame containing phenotype and sample information.
densityEstimate:: Gets the matrix containing the density estimate.
densityQuantiles:: Gets the quantiles of the nonzero values in the density estimate.

## Construct a completely fake example
densmat <- matrix(rnorm(600), nrow = 20, ncol = 30)
colnames(densmat) <- 1:ncol(densmat)
rownames(densmat) <- seq(350, by = 0.005, length.out = nrow(densmat))
cmsobj <- new("CMSproc", density = densmat)
head(densityEstimate(cmsobj))

## Takes about 20s to run
## Not run: 

data(cmsRawExample)
cmsProc <- bakedpi(cmsRawExample,
                    dbandwidth = c(0.01, 10), dgridstep = c(0.01, 1),
                    dortalign = TRUE, mzsubset = c(500,510))
cmsProc

## End(Not run)