custom.featureTable: Import Custom Feature Table

In HuanLab/JPA:

Import Custom Feature Table

Description

Perform IPA analysis using user provided feature table in CSV format generated by MS-DIAL, MZmine2, etc instead of using XCMS feature table. Also annotates each feature as either level 1 or 2.

Usage

custom.featureTable(dir, FTdir, mz.tol = 10)

Arguments

dir	Directory of folder containing all .mzXML files of interest. This folder must contain only relevant .mzXML files of DDA sample(s).
FTdir	Directory containing feature table in CSV format.
mz.tol	Mass tolerance in ppm used to identify level 1 features by matching the feature's mz against all ms2 precursor mz. Default = 10.

Details

The number of mzXML files to process must be equal to the number of input CSV files where each CSV file contains features extracted from each mzXML file. Note: for multi-sample analysis, the feature table provided must not be aligned. The existing feature table must be in CSV format and contains only the following columns in order: "mz", "rt", "rtmin", "rtmax", "intensity".

Value

Returns a feature table in dataframe format, containing the following columns in order: "mz", "rt", "rtmin", "rtmax", "maxo", "sample", "level" where "maxo" is the feature peak intensity. Also returns an XCMS object that is used by functions later in the IPA workflow.

Author(s)

Sam Shen, Jian Guo, Tao Huan

Examples

library(IPA)
dir = "X:/Users/Sam_Shen/IPAtest_20210330/singleDDA"
FTdir = "X:/Users/Sam_Shen/IPAtest_20210330/singleDDA"
featureTable <- read.featureTable(dir = dir, FTdir = FTdir)

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