Funcition for performing unsupervised conformational signature analysis. This performs PCA on the TRE values of the RexDifferentialList and returns the PCA object and the TRE values in wide format.

Funcition for performing unsupervised conformational signature analysis. This performs PCA on the TRE values of the RexDifferentialList and returns the PCA object and the TRE values in wide format.

UnsupervisedCSA(
  RexDifferentialList,
  quantity = "TRE",
  states,
  whichTimepoint = 600,
  pca_params = list(scale = FALSE, center = TRUE)
)

Arguments

RexDifferentialList

A list of RexDifferential objects

quantity

The quantity to use for the analysis. Default is "TRE"

states

The state name to use for the analysis/ e.g. ligand used in differential analysis

whichTimepoint

The timepoint to use for the analysis. Default is 600

pca_params

The parameters to use for the PCA. Default is list(scale = FALSE, center = TRUE)

Value

A list containing the PCA object and the TRE values in wide format

Examples

library("RexMS")
data("out_lxr_compound_proccessed")
data("LXRalpha_compounds")

states <- names(LXRalpha_compounds)


ucsa <- UnsupervisedCSA(out_lxr_compound_proccessed,
                       quantity = "TRE",
                       states = states,
                       whichTimepoint = 600,
                       pca_params = list(scale = FALSE,
                                         center = TRUE))