mzdata_raw: Feature detection using xcms.
In brgordon17/coralclass: Metabolomics Classification of Stressed Coral From Heron Island 2011

Description Usage Arguments Details Value Note Author(s) See Also

Method used by Gordon et. al. to extract LCMS features from .mzXML files using xcms.

1	mzdata_raw(saveoutput = FALSE, outputname = "example-mzdata-raw", ...)

`saveoutput`	Logical indicating if output should be saved
`outputname`	The name of the output file to be saved if `TRUE`
`...`	Other arguments passed on to individual methods

This function was used to extract features from .mzXML data. The function creates an xcmsSet object, groups peaks, corrects for retention time drift, re-groups the peaks, fills missing peaks, annotates adducts and isotopes, before saving the output to a .csv file in /data-raw.

Returns a dataframe of class tbl_df

mzdata_raw() was not intended to be used outside of this package. To keep the size of this package small, only a small example subset of the raw LCMS .mzXML data is made available in ./data-raw/example_mzxml_data/. The full data set is available from the package author.

Benjamin R. Gordon

xcmsSet annotate

brgordon17/coralclass documentation built on June 15, 2020, 9:21 p.m.