xcms_orbi_A: xcms_orbi_A
In Mystilivia/SDjoygret: Testing R Package

Description Usage Arguments

This function perform the first steps of metabolomic analysis : xcmsSet and two iteration with group and retcor to end with fillpeaks. The resulting output is a xcms set object. Parameters are saved in a table.

1 2	xcms_orbi_A() xcms_orbi_A()

`File_list`	File list to pass to xcmsSet method = 'centWave', ppm=7, peakwidth=c(4,20), snthresh=10, prefilter=c(4,1000), mzdiff=0.015, fitgauss=F, nSlaves = 4, phenoData = Sample.Metadata) If phenoData is a dataframe with at lest a 'class' column. Could be any number of columns but in files sample order. If 'injectionorder' and 'batch" columns are presents, those will be use to order en color QCs plot.
`xcmsSet_param`	xcmsSet parameters (can be any parameters formated like this : c(method="centWave", "ppm=7)).
`Results.dir.name`	Name of the subfolder to store results.
`bw_param`	Vector for bw settings to use in 1, 2 and 3 iteration : c(1, 2, 3).
`mzwid_param`	mzwid parameter to use.
`minfrac_param`	minfrac parameter to use.
`profStep_param`	profStep parameter to use.
`STDs_data`	A dataframe of m/z to plot with at least one "mz" named column.
`STDs_EIC`	Should EIC of ions list be plotted.
`QCs_Graph`	Logical to determine of QCs graphs needs to be saved.