rtmsEcho (version 0.2.4)

getTIC: Extract a total ion chromatogram (TIC) from a Wiff file

Description

Extract a total ion chromatogram (TIC) from a Wiff file

Usage

getTIC(wiff, index = 1)

Value

A data frame containing the TIC data (see Details)

Arguments

wiff

A wiff reader object of class rtmsWiffReader

index

The particular run within the wiff file for which the TIC should be extracted. Defaults to 1, the first (and often only) run.

Details

The total ion chromatogram data in a .wiff file contains data for every moment at which the EchoMS took a measurement. Each measurement is represented by a single row in the returned data frame, with the following four values:

• time: The time (in seconds) after the beginning of the run at which the measurement was taken

• intensity: The total ion intensity across all masses measured

• full: Either 0 (indicating data is stored as a discrete set of targeted intensities) or 1 (indicating the data is stored as a compressed full spectrum)

• offset: The binary offset within this run's data block in the associated .wiff.scan file at which this measurement's raw data can be found

• size: The size (in bytes) of this measurment's raw data in the associated .wiff.scan file.

Examples

wiff <- exampleWiff

tic <- getTIC(wiff)

# Plot the first 60 seconds of the total ion chromatgram using [ggplot2]
ggplot2::ggplot(tic,ggplot2::aes(x=time,y=intensity))+
	ggplot2::geom_line(color="red")+
	ggplot2::xlim(0,60)