processAssayXcmsSet {Risa} | R Documentation

## Build an xcmsSet object given a mass spectrometry assay and considering all factors defined

### Description

`processAssayXcmsSet` retrieves an xcmsSet object given and ISA-tab object and one of its assay filenames.

### Usage

    processAssayXcmsSet(isa, assay.filename, ...)

### Arguments

`isa` | an ISA object, as retrieved by the function `readISAtab`
`assay.filename` | a boolean indicating to show messages for the different steps, if TRUE, or not to show them, if FALSE
`...` | extra arguments that can be pass down to the xcmsSet function from the xcms package

### Value

the xcmsSet object built from the assay metadata, considering all the factors defined, and data files

### Author(s)

Steffen Neumann, Alejandra Gonzalez-Beltran / Maintainer: Alejandra Gonzalez-Beltran isatools@googlegroups.com

### See Also

`readISAtab`

### Examples

     faahkoISA = readISAtab(find.package("faahKO"))
     assay.filename <- faahkoISA["assay.filenames"][[1]]
     xset = processAssayXcmsSet(faahkoISA, assay.filename)

[Package Risa version 1.26.0 Index]