xcms_orbi_GRT: xcms_orbi_GRT

In Mystilivia/SDjoygret: Testing R Package

Description

This function simplify workflow from peak grouping and retention time correction to PCA analysis. Function will perform group -> retcor -> group -> retcor -> group and return EIC for standards across all samples and extract standards from peaks table, giving also ppm deviation for each std for diagnostic.

Usage

xcms_orbi_GRT(xcms_set_obj, Results.dir.name="Default", bw_param=c(25, 10, 0.7), mzwid_param=0.005, minfrac_param=0.25, profStep_param=0.8)
xcms_orbi_GRT()

Arguments

File_list	File list to pass to xcmsSet method = 'centWave', ppm=7, peakwidth=c(4,20), snthresh=10, prefilter=c(4,1000), mzdiff=-0.001, fitgauss=F, nSlaves = 4
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
Sample.Metadata	Dataframe with samples names and metadata
Grouping.factor	Col.number of Sample.Metadata to use for ACP colors (can be a vector)

Mystilivia/SDjoygret documentation built on May 7, 2019, 5:17 p.m.