In cbg-ethz/timeseriesNEM: Map an Observational Time Series onto a Static NEM Signalling Network

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(nem)
library(timeseriesNEM)

Let's generate a random NEM with 10 S-nodes.

set.seed(1)
nem.res <- timeseriesNEM:::sample_random_NEM_and_data(n = 10, m = 1000)
plot(nem.res, transitiveReduction = TRUE)

Say we perturb S4. Which other S-nodes would then be perturbed? Generate an observational effect profile from this perturbation.

test <- timeseriesNEM:::generate_tsNEM_dataset(nem.res, "S4")
test$affectedSgenes

Use timeseriesNEM to infer from the observational effect profile which S-nodes were affected by the perturbation.

tsNEM(test$nemObject, test$logDensities)

cbg-ethz/timeseriesNEM documentation built on May 14, 2019, 5 a.m.