analyzeIntensityCutoffsDistr: Calculate effects of applying intensity-level cutoffs on mass...

In kbseah/mass2adduct: Mass Spectrometry Imaging Molecular Adduct Finder

Description

Given a table of total intensities per mass peak, produced by function sumPeakIntensities, calculate the number of peaks retained if a minimum intensity cutoff is applied (either as absolute value or as percentage of the maximum intensity value observed). To do the inverse, i.e. find the corresponding intensity value for a desired number of peaks, use the quantile function.

Usage

analyzeIntensityCutoffsDistr(df, by = c("intensities", "counts"),
  value = NULL, pc = 1, plot = TRUE, report.peaks = FALSE)

Arguments

df	data.frame of three columns: peaks, counts, intensities, produced by function sumPeakIntensities or by external script msicsvprofiler.pl
by	string; Apply cutoff by intensities or counts (default: intensities)
value	numeric; Minimum intensity/counts cutoff to apply
pc	numeric; Percent intensity/counts cutoff to apply (ignored if value supplied) (Default: 1)
plot	logical; Plot empirical CDF?
report.peaks	logical; Return peaks that are above cutoff? (default: no)

Value

data.frame summarizing the number of peaks above the specified cutoff and a plot of the distribution with cutoff overlaid as a vertical line. If option report.peaks is used, then the a vector of peaks above the cutoff is returned instead.

See Also

analyzeIntensityCutoffsCumul does a similar analysis, but orders the peaks by intensity and takes the cumulative sum.

sumPeakIntensities function to generate the data.frame of total intensities and pixel counts per peak from a msimat object.

kbseah/mass2adduct documentation built on June 9, 2021, 9:20 p.m.