GCIMSChromatogramSet class

GCIMSChromatogramSet is an S4 class to store one GCIMSChromatogram per sample of a GCIMSDataset, together with a copy of pData() so plots can use the dataset's annotations.

Samples are not required to share a common retention time axis: each chromatogram keeps its own, exactly as extracted from its sample. No interpolation is performed.

# S4 method for class 'GCIMSChromatogramSet'
sampleNames(object)

# S4 method for class 'GCIMSChromatogramSet,ANY'
sampleNames(object) <- value

# S4 method for class 'GCIMSChromatogramSet'
pData(object)

# S4 method for class 'GCIMSChromatogramSet'
length(x)

# S4 method for class 'GCIMSChromatogramSet'
x[[i]]

# S4 method for class 'GCIMSChromatogramSet,ANY'
plot(x, color_by = "SampleID", ...)

Arguments

object

A GCIMSChromatogramSet object

value

A character vector of length the number of chromatograms with the new sample names

x

A GCIMSChromatogramSet object to plot

i

A number or a string with the sample index or name

color_by

The name of a pData(x) column (or "SampleID") used to color the chromatograms

...

Ignored

Value

A character vector with the sample names

The GCIMSChromatogramSet object, with samples renamed in both chromatograms and pData()

A tibble with the phenotype data, or NULL if not set

An integer with the number of chromatograms

The GCIMSChromatogram of the requested sample

A ggplot2 plot object

Functions

  • sampleNames(GCIMSChromatogramSet): Get the sample names

  • sampleNames(object = GCIMSChromatogramSet) <- value: Set the sample names

  • pData(GCIMSChromatogramSet): Get the phenotype data

  • length(GCIMSChromatogramSet): Number of chromatograms (samples) in the set

  • [[: Extract the chromatogram of a single sample

  • plot(x = GCIMSChromatogramSet, y = ANY): plot method

Slots

chromatograms

A named list of GCIMSChromatogram objects, one per sample, named after their SampleID.

pData

A DataFrame with the phenotype data, or NULL.