Plot m/z and RT deviations for QC purposes without external reference data
Source:R/plotQC.R
plotQC.Rd
Use "democracy" to determine the average m/z and RT deviations for a grouped xcmsSet, and dependency on sample or absolute m/z
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
List with four matrices, each of dimension features * samples: "mz": median mz deviation for each sample "mzdev": median mz deviation for each sample "rt": median RT deviation for each sample "rtdev": median RT deviation for each sample