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

Description Usage Arguments Value See Also

View source: R/analyzeIntensityCutoffsDistr.R

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

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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 Aug. 20, 2019, 12:18 p.m.