Write optional disk outputs for longitudinal mixed-effects analyses

Source: R/methylationLME_steps.R

Write optional serialized outputs, summary tables, significant interaction tables, and annotated results from the longitudinal mixed-effects workflow.

writeMethylationLMEOutputs(
  modelResults,
  modelSummaries,
  annotatedResults,
  significantInteractions = NULL,
  outputRData,
  summaryTxtDir,
  significantInteractionDir,
  annotatedLMEOut,
  saveTxtSummaries = TRUE,
  saveSignificantInteractions = FALSE,
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_methylationLME.txt"
)

Arguments

modelResults

Object returned by fitMethylationLMEModels().

modelSummaries

Object returned by summarizeMethylationLMEModels().

annotatedResults

Object returned by annotateMethylationLMESummaries() or a compatible data frame.

significantInteractions

Object returned by collectSignificantInteractionsMethylationLME() or NULL.

outputRData

Character. Directory used for serialized model and summary outputs.

summaryTxtDir

Character. Directory used for tab-delimited summary tables.

significantInteractionDir

Character. Directory used for significant interaction coefficient tables.

annotatedLMEOut

Character. Directory used for the annotated summary XLSX workbook.

saveTxtSummaries

Logical. If TRUE, write tab-delimited summary tables.

saveSignificantInteractions

Logical. If TRUE, write significant interaction coefficient tables.

verbose

Logical. If TRUE, emit progress messages with message().

logs

Logical. If TRUE, write the same messages to a log file.

log_dir

Character or NULL. Directory used for the log file when logs = TRUE.

log_file

Character. File name used when logs = TRUE.

Value

A list with class "dnaEPICO_methylationLME_paths" containing the paths of the files written to disk.

Examples

ex <- dnaEPICO:::exampleMethylationLMEStateDnaEpico()
annotation_data <- annotateMethylationLMESummaries(
  modelSummaries = ex$modelSummaries,
  annotationObject = ex$annotationData,
  annotationCols = "Name,chr,pos",
  verbose = FALSE,
  logs = FALSE
)
significant_hits <- collectSignificantInteractionsMethylationLME(
  modelResults = ex$modelResults,
  pvalThreshold = 1,
  verbose = FALSE,
  logs = FALSE
)
output_paths <- writeMethylationLMEOutputs(
  modelResults = ex$modelResults,
  modelSummaries = ex$modelSummaries,
  annotatedResults = annotation_data,
  significantInteractions = significant_hits,
  outputRData = file.path(ex$tempDir, "models"),
  summaryTxtDir = file.path(ex$tempDir, "summary"),
  significantInteractionDir = file.path(ex$tempDir, "significant"),
  annotatedLMEOut = file.path(ex$tempDir, "annotated"),
  saveTxtSummaries = TRUE,
  saveSignificantInteractions = TRUE,
  verbose = FALSE,
  logs = FALSE
)
names(output_paths)
#> [1] "modelFiles"                  "summaryFiles"               
#> [3] "summaryTxtFiles"             "significantInteractionFiles"
#> [5] "annotatedLME"