generateIonChromatogram: Generate ion chromatogram from raw data points

In peakPantheR: Peak Picking and Annotation of High Resolution Experiments

Description

On the input raw data, aggregate intensites across the mz range at each retention time to generate an ion chromatogram: sum for EIC/TIC, max, min or mean. The number of data points returned correspond to the number of unique scans/retention time measurements in the input data

Usage

generateIonChromatogram(ROIDataPoint, aggregationFunction = "sum")

Arguments

ROIDataPoint	(data.frame) retention time "rt", mass "mz" and intensity "int" (as column) of each raw data points (as row) to use for the ion chromatogram
aggregationFunction	(str) Function to use in order to aggregate intensities across mz in each scan. One of sum, max, min, mean

Value

A data.frame of retention time "rt" and aggregated intensities "int"

Examples

## Not run: 
## Input data points
in_rt   <- c(3362.102, 3362.102, 3363.667, 3363.667, 3365.232, 3365.232, 3366.797, 3366.797,
             3368.362, 3368.362)
in_mz   <- c(496.2, 497.2, 496.2, 497.2, 496.2, 497.2, 496.2, 497.2, 496.2, 497.2)
in_int  <- c(39616, 11432, 63344, 18224, 107352, 30936, 182144, 51776, 295232, 81216)
input_ROIDataPoints <- data.frame(rt=in_rt, mz=in_mz, int=in_int)

## Aggregate mz to generate EIC
EIC <- generateIonChromatogram(input_ROIDataPoints, aggregationFunction='sum')
EIC
#         rt    int
# 1 3362.102  51048
# 2 3363.667  81568
# 3 3365.232 138288
# 4 3366.797 233920
# 5 3368.362 376448

## End(Not run)

peakPantheR documentation built on May 1, 2019, 10:53 p.m.