Write optional disk outputs for one-timepoint GLM analyses — writeMethylationGLMOutputs • dnaEPICO

Write optional serialized outputs, summary tables, significant-CpG tables, and annotated results from the one-timepoint GLM workflow.

writeMethylationGLMOutputs(
  modelResults,
  modelSummaries,
  annotatedResults,
  significantCpGs = NULL,
  outputRData,
  summaryTxtDir,
  significantCpGDir,
  annotatedGLMOut,
  saveTxtSummaries = TRUE,
  saveSignificantCpGs = FALSE,
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_methylationGLM.txt"
)

Arguments

modelResults: Object returned by fitMethylationGLMModels().
modelSummaries: Object returned by summarizeMethylationGLMModels().
annotatedResults: Object returned by annotateMethylationGLMSummaries() or a compatible data frame.
significantCpGs: Object returned by collectSignificantCpGsMethylationGLM() or NULL.
outputRData: Character. Directory used for serialized model and summary outputs.
summaryTxtDir: Character. Directory used for tab-delimited summary tables.
significantCpGDir: Character. Directory used for significant-CpG coefficient tables.
annotatedGLMOut: Character. Directory used for the annotated summary XLSX workbook.
saveTxtSummaries: Logical. If TRUE, write tab-delimited summary tables.
saveSignificantCpGs: Logical. If TRUE, write significant-CpG 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_methylationGLM_paths" containing the paths of the files written to disk.

Examples

ex <- dnaEPICO:::exampleMethylationGLMStateDnaEpico()
annotation_data <- annotateMethylationGLMSummaries(
  modelSummaries = ex$modelSummaries,
  annotationObject = ex$annotationData,
  annotationCols = "Name,chr,pos",
  verbose = FALSE,
  logs = FALSE
)
significant_cpgs <- collectSignificantCpGsMethylationGLM(
  modelResults = ex$modelResults,
  pvalThreshold = 1,
  verbose = FALSE,
  logs = FALSE
)
output_paths <- writeMethylationGLMOutputs(
  modelResults = ex$modelResults,
  modelSummaries = ex$modelSummaries,
  annotatedResults = annotation_data,
  significantCpGs = significant_cpgs,
  outputRData = file.path(ex$tempDir, "models"),
  summaryTxtDir = file.path(ex$tempDir, "summary"),
  significantCpGDir = file.path(ex$tempDir, "significant"),
  annotatedGLMOut = file.path(ex$tempDir, "annotated"),
  saveTxtSummaries = TRUE,
  saveSignificantCpGs = TRUE,
  verbose = FALSE,
  logs = FALSE
)
names(output_paths)
#> [1] "modelFiles"          "summaryFiles"        "summaryTxtFiles"    
#> [4] "significantCpGFiles" "annotatedGLM"