XSet2MSet: Converts xset object from XCMS to mSet object for...

In xia-lab/MetaboAnalystR: An R Package for Comprehensive Analysis of Metabolomics Data

Converts xset object from XCMS to mSet object for MetaboAnalyst

Description

This function converts processed raw LC/MS data from XCMS to a usable data object (mSet) for MetaboAnalyst. The immediate next step following using this function is to perform a SanityCheck, and then further data processing and analysis can continue.

Usage

XSet2MSet(xset, dataType, analType, paired = F, format, lbl.type)

Arguments

xset	The name of the xcmsSet object created.
dataType	The type of data, either list (Compound lists), conc (Compound concentration data), specbin (Binned spectra data), pktable (Peak intensity table), nmrpeak (NMR peak lists), mspeak (MS peak lists), or msspec (MS spectra data).
analType	Indicate the analysis module to be performed: stat, pathora, pathqea, msetora, msetssp, msetqea, mf, cmpdmap, smpmap, or pathinteg.
paired	Logical, is data paired (T) or not (F).
format	Specify if samples are paired and in rows (rowp), unpaired and in rows (rowu), in columns and paired (colp), or in columns and unpaired (colu).
lbl.type	Specify the data label type, either categorical (disc) or continuous (cont).

xia-lab/MetaboAnalystR documentation built on April 15, 2024, 12:16 p.m.