peakRangeSum: raw eic signal intensity and mass summation and spike...

Description Usage Arguments Value

View source: R/peakRangeSum.R

Description

raw eic signal intensity and mass summation and spike removal.

Usage

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peakRangeSum(peakRange = NULL, spikeScans = 2, rtDevModel = NULL,
gaussAlpha = NULL, 
maxEmptyRt = 7)

Arguments

peakRange

matrix consisting of 5 columns:

  1. mass-to-charge values

  2. intensity

  3. retention time (in seconds)

  4. scan number

spikeScans

numeric number of scans <= a spike. Any peaks <= this value will be removed (default = 2).= FALSE

rtDevModel

loess model to correct retention times.

gaussAlpha

numeric alpha value for smth.gaussian of smoother package. If supplied gaussian smoothing will be performed (suggested value = 16).

maxEmptyRt

numeric maximum size of empty retention time beyond which missing values will be zero-filled

Value

matrix with masses and intensities summed by retention time and retention time correction based on the loess model supplied, the matrix has spikes removed (consecutive non-zero intensity values <= spikeScans in length), empty time segments are zero filled (> 3 seconds), optionally gaussian smoothed using the linksmth.gaussian function of the smoother package and is also subset based on the minimum and maximum retention time windows supplied (rtWin). The returned matrix consists of 5 columns:

  1. average mass-to-charge values by unique retention time in supplied peakRange table

  2. maximum intensity values by unique retention time in supplied peakRange table

  3. loess model corrected retention times

  4. original retention time values

  5. scan number by unique retention time in supplied peakRange table


adductomicsR documentation built on Nov. 8, 2020, 4:49 p.m.