Description Usage Arguments Value See Also

View source: R/analyzeIntensityCutoffsDistr.R

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.

1 2 |

`df` |
data.frame of three columns: peaks, counts, intensities, produced
by function |

`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) |

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.

`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.

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