peakRangeSum {adductomicsR} | R Documentation

## raw eic signal intensity and mass summation and spike removal.

### Description

raw eic signal intensity and mass summation and spike removal.

### Usage

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

### Arguments

`peakRange` | matrix consisting of 5 columns: mass-to-charge values intensity retention time (in seconds) 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 link`smth.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

[Package adductomicsR version 1.0.0 Index]