Function to calculate the uncertainty in the TRE values by sampling the posterior distribution of the Rex parameters. Typically used to obtain uncertainty in the conformational signatures.

Function to calculate the uncertainty in the TRE values by sampling the posterior distribution of the Rex parameters. Typically used to obtain uncertainty in the conformational signatures.

sampleTREuncertainty(
  HdxData,
  RexParamsList,
  quantity = "TRE",
  states,
  whichChain = 1,
  whichSamples = seq.int(1, 50),
  whichTimepoint = 600,
  num_montecarlo = 5000
)

Arguments

HdxData

The HdxData object

RexParamsList

A list of RexParams 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

whichChain

The chain to use for the analysis. Default is 1

whichSamples

The samples to use for the analysis. Default is seq.int(1, 50)

whichTimepoint

The timepoint to use for the analysis. Default is 600.

num_montecarlo

The number of montecarlo samples to use for the analysis

Value

A data frame containing the TRE values and the residue number over monte carlo interations

Examples

  
if (FALSE) {
library("RexMS")
data("LXRalpha_processed")
data("rex_lxr")
data("LXRalpha_compounds")

states <- names(LXRalpha_compounds)

TRE_dist <- sampleTREuncertainty(HdxData = LXRalpha_processed,
                               RexParamsList = rex_lxr,
                               quantity = "TRE",
                               states = states,
                               whichChain = 1,
                               whichSamples = seq.int(1, 50),
                               whichTimepoint = 600,
                               num_montecarlo = 5000)
                               


}