ms2.tofeaturetable: Assigns MS2 to Corresponding Features

In HuanLab/JPA:

Assigns MS2 to Corresponding Features

Description

Extracts and assigns MS2 spectra to features in feature table.

Usage

ms2.tofeaturetable(data, featureTable, rt.tol = 30, mz.tol = 0.01)

Arguments

data	"MSdata" object generated in previous steps.
featureTable	Feature table dataframe generated in previous steps.
rt.tol	Retention time tolerance (seconds) used in MS2 assignment to feature table. Default = 30.
mz.tol	Mass tolerance tolerance (Da) used in MS2 assignment to feature table. Default = 0.01.

Value

Returns a feature table with additional columns containing MS2 fragment m/z and intensity information for each feature.

Author(s)

Sam Shen, Jian Guo, Tao Huan

Examples

library(IPA)
dir = "X:/Users/Sam_Shen/IPAtest_20210330/singleDDA"
featureTable <- peak.picking(dir = dir, mz.tol = 10, ppm=10, peakwidth=c(5,20), mzdiff = 0.01,
                             snthresh = 6, integrate = 1, prefilter = c(3,100), noise = 100)
featureTable <- find.level3features(data = MSdata)
featureTable <- ms2.tofeaturetable(data = MSdata, featureTable = featureTable)

HuanLab/JPA documentation built on April 14, 2023, 12:53 p.m.