feature.annotation: Feature Annotation

In HuanLab/JPA:

Feature Annotation

Description

Annotates each feature in feature table with MS2 fragment information using the dot product method.

Usage

feature.annotation(featureTable, lib_directory, lib_name, dp = 0.7, ms1.tol = 0.01, ms2.tol = 0.02)

Arguments

featureTable	FeatureTable generated by the ms2.tofeaturetable() function containing all features with MS2 fragment information.
lib_directory	Directory containing the annotation library.
lib_name	Name of annotation library. Must be in msp format.
dp	Dot product threshold for annotating features. Default = 0.7.
ms1.tol	MS1 precursor m/z tolerance used in performing dot product calculation. Default = 0.01.
ms2.tol	MS2 m/z tolerance used in performing dot product calculation. Default = 0.02.

Value

Returns the input feature table with additional columns containing metabolite names and dot product scores for each annotated metabolite.

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)

lib_directory <- "E:/SAM"
lib_name <- "convertedLibraryNeg.msp"
featureTable <- ms2.tofeaturetable(data = MSdata, featureTable = featureTable)
featureTable <- feature.annotation(featureTable = featureTable, lib_directory = lib_directory, lib_name = lib_name, dp = 0.1)

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