scp 1.14.0
This vignette briefly recaps the main concepts of QFeatures
on which
scp
relies. More in depth information is to be found in the
QFeatures
vignettes.
QFeatures
classThe QFeatures
class (Gatto and Vanderaa (2023)) is based on the
MultiAssayExperiment
class that holds a collection of
SummarizedExperiment
(or other classes that inherits from it)
objects termed assays. The assays in a QFeatures
object have a
hierarchical relation: proteins are composed of peptides, themselves
produced by spectra, as depicted in figure below.
A more technical representation is shown below, highlighting that each
assay is a SummarizedExperiment
(containing the quantitative data,
row and column annotations for each individual assay), as well as a
global sample annotation table, that annotates cells across all
assays.