Exporing Results"

In TreatmentPatterns: Analyzes Real-World Treatment Patterns of a Study Population of Interest

knitr::opts_chunk$set(echo = TRUE)

withr::local_envvar(
  R_USER_CACHE_DIR = tempfile(),
  EUNOMIA_DATA_FOLDER = Sys.getenv("EUNOMIA_DATA_FOLDER", unset = tempfile())
)

Exporting result objects

The export function allows us to export the generated result objects from computePathways. There are several arguments that we can change to alter the behavior, depending on what we are allowed to share.

minCellCount and censorType

Let's say we are only able to share results of groups of subjects that have at least 5 subjects in them.

results <- export(
  andromeda = defaultSettings,
  minCellCount = 5
)

We can also choose between different methods how to handle pathways that fall below are specified minCellCount. These types are 1) "cellCount", 2) "remove", and 3) "mean".

We could say we want to censor all pathways that fall below the minCellCount to be censored to the minCellCount.

resultsA <- export(
  andromeda = minEra60,
  minCellCount = 5,
  censorType = "minCellCount"
)

Or we could completely remove them

resultsB <- export(
  andromeda = minEra60,
  minCellCount = 5,
  censorType = "remove"
)

Or finally we can censor them as the mean of all the groups that fall below the minCellCount.

resultsC <- export(
  andromeda = minEra60,
  minCellCount = 5,
  censorType = "mean"
)

ageWindow

We can also specify an age window.

resultsD <- export(
  andromeda = splitAcuteTherapy,
  minCellCount = 5,
  censorType = "mean",
  ageWindow = 3
)

Or a collection of ages.

resultsE <- export(
  andromeda = splitAcuteTherapy,
  minCellCount = 5,
  censorType = "mean",
  ageWindow = c(0, 18, 25, 30, 40, 50, 60, 150)
)

archiveName

Finally we can also specify an archiveName which is the name of a zip-file to zip all our output csv-files to.

resultsF <- export(
  andromeda = includeEndDate,
  minCellCount = 5,
  censorType = "mean",
  ageWindow = 3,
  archiveName = "output.zip"
)

Patient-Level Export

We can also export patient-level data to use for internal analyses. Obviously these results are not share-able. Currently the results are only exported as csv-files.

exportPatientLevel(
  andromeda = outputEnv,
  outputPath = tempdir()
)

We go into evaluating the output of the files in the Evaluating Output vignette.

TreatmentPatterns documentation built on June 8, 2025, 11:18 a.m.