processAssayXcmsSet

 an ISA object, as retrieved by the function <code>readISAtab</code>

 a boolean indicating to show messages for the different steps, if TRUE, or not to show them, if FALSE

assay.filename

 extra arguments that can be pass down to the xcmsSet function from the xcms package


  <code>processAssayXcmsSet</code> retrieves an xcmsSet object given and ISA-tab object and one of its assay filenames.


The Investigation / Study / Assay (ISA) tab-delimited
format is a general purpose framework with which to collect and communicate
complex metadata (i.e. sample characteristics, technologies used, type
of measurements made) from experiments employing a combination of
technologies, spanning from traditional approaches to high-throughput
techniques. Risa allows to access metadata/data in ISA-Tab format and
build Bioconductor data structures. Currently, data generated from microarray,
flow cytometry and metabolomics-based (i.e. mass spectrometry) assays are supported.
The package is extendable and efforts are undergoing to support metadata associated to proteomics assays.

Alejandra GonzalezBeltran

Risa

Converting experimental metadata from ISA-tab into Bioconductor data structures

processAssayXcmsSet function

an ISA object, as retrieved by the function <code>readISAtab</code>

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

<code>processAssayXcmsSet</code> retrieves an xcmsSet object given and ISA-tab object and one of its assay filenames.

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

Description

Usage

Arguments

Value

See Also

Examples