cont.index: Continuity index

In yufree/apLCMS: Adaptive processing of LC-MS data

Continuity index

Description

This is an internal function. It uses continuity index (or "run filter") to select putative peaks from EIC.

Usage

cont.index(newprof, min.pres = 0.6, min.run = 5)

Arguments

newprof	The matrix containing m/z, retention time, intensity, and EIC label as columns.
min.pres	Run filter parameter. The minimum proportion of presence in the time period for a series of signals grouped by m/z to be considered a peak.
min.run	Run filter parameter. The minimum length of elution time for a series of signals grouped by m/z to be considered a peak.

Details

This is the run filter described in Yu et al Bioinformatics 2009.

Value

A list is returned.

new.rec	The matrix containing m/z, retention time, intensity, and EIC label as columns after applying the run filter.
height.rec	The vector of peak heights.
time.range.rec	The vector of peak retention time span.
mz/pres.rec	The vector of proportion of non-missing m/z.

Author(s)

Tianwei Yu <[e-mail]>

References

Bioinformatics. 25(15):1930-36. BMC Bioinformatics. 11:559.

yufree/apLCMS documentation built on May 19, 2024, 1:22 p.m.