peakFind: Intensities and RI matrices

View source: R/peakFind.R

peakFindR Documentation

Intensities and RI matrices

Description

This function returns a list of the intensities and RI matrices that were searched.

Usage

peakFind(samples, Lib, cor_RI, columns = NULL, showProgressBar = FALSE)

Arguments

samples

A tsSample object created by ImportSamples function.

Lib

A tsLib object created by ImportLibrary function with corrected RI values. See medianRILib.

cor_RI

A matrix of correlating selective masses RI for every sample. See sampleRI.

columns

Either NULL, a character vector, or an integer vector. In most cases, leave it as NULL. This parameter is used to configure the column names or positions of RI text files. See the documentation on the text2bin function for further details.

showProgressBar

Logical. Should the progress bar be displayed?

Value

A tsMSdata object.

Author(s)

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

See Also

ImportSamples, ImportLibrary, medianRILib, sampleRI, tsMSdata, tsLib, tsSample

Examples

require(TargetSearchData)
data(TSExample)

# get RI file path
RI.path <- tsd_data_path()
refLibrary <- ImportLibrary(tsd_file_path("library.txt"))

# update RI file path
RIpath(sampleDescription) <- RI.path

peakData <- peakFind(sampleDescription, refLibrary, corRI)
# show peak Intensities. 
head(Intensity(peakData), 2)

# How to get intensities for a particular metabolite
# just select the identifier. Here extract the intensities
# for the first metabolite in the library
IntMatrix <- Intensity(peakData)[[1]]


acinostroza/TargetSearch documentation built on May 5, 2024, 10:14 a.m.