xcms (version 1.48.0)

plotQC: Plot m/z and RT deviations for QC purposes without external reference data

Description

Use "democracy" to determine the average m/z and RT deviations for a grouped xcmsSet, and dependency on sample or absolute m/z

Usage

plotQC(object, sampNames, sampColors, sampOrder, what)

Arguments

object

A grouped xcmsSet

sampNames

Override sample names (e.g. with simplified names)

sampColors

Provide a set of colors (default: monochrome ?)

sampOrder

Override the order of samples, e.g. to bring them in order of measurement to detect time drift

what

A vector of which QC plots to generate. "mzdevhist": histogram of mz deviations. Should be gaussian shaped. If it is multimodal, then some peaks seem to have a systematically higher m/z deviation "rtdevhist": histogram of RT deviations. Should be gaussian shaped. If it is multimodal, then some peaks seem to have a systematically higher RT deviation "mzdevmass": Shows whether m/z deviations are absolute m/z dependent, could indicate miscalibration "mzdevtime": Shows whether m/z deviations are RT dependent, could indicate instrument drift "mzdevsample": median mz deviation for each sample, indicates outliers "rtdevsample": median RT deviation for each sample, indicates outliers

Value

No return value

Details

plotQC() is a warpper to create a set of diagnostic plots. For the m/z deviations, the median of all m/z withon one group are assumed.

Examples

library(faahKO)
xsg <- group(faahko)

plotQC(xsg, what="mzdevhist")
plotQC(xsg, what="rtdevhist")
plotQC(xsg, what="mzdevmass")
plotQC(xsg, what="mzdevtime")
plotQC(xsg, what="mzdevsample")
plotQC(xsg, what="rtdevsample")