Run preprocessingPheno.R

preprocessingPheno(
  phenoFile = "data/preprocessingMinfiEwasWater/phenoLC.csv",
  sepType = "",
  betaPath =
    "rData/preprocessingMinfiEwasWater/metrics/beta_NomFilt_MSetF_Flt_Rxy_Ds_Rc.RData",
  mPath = "rData/preprocessingMinfiEwasWater/metrics/m_NomFilt_MSetF_Flt_Rxy_Ds_Rc.RData",
  cnPath =
    "rData/preprocessingMinfiEwasWater/metrics/cn_NomFilt_MSetF_Flt_Rxy_Ds_Rc.RData",
  SampleID = "Sample_Name",
  timeVar = "Timepoint",
  timepoints = "1,2",
  combineTimepoints = "1,2",
  outputPheno = "data/preprocessingPheno",
  outputRData = "rData/preprocessingPheno/metrics",
  outputRDataMerge = "rData/preprocessingPheno/mergeData",
  sexColumn = "Sex",
  outputLogs = "logs",
  outputDir = "data/preprocessingPheno"
)

Arguments

phenoFile: Character. Path to phenotype file.
sepType: Character. Field separator for phenotype file.
betaPath: Character. Path to beta-values RData file.
mPath: Character. Path to M-values RData file.
cnPath: Character. Path to copy number RData file.
SampleID: Character. Sample identifier column name.
timeVar: Character. Time variable column name.
timepoints: Character. Timepoints to retain.
combineTimepoints: Character. Timepoints to combine.
outputPheno: Character. Output directory for processed phenotype files.
outputRData: Character. Output directory for metric RData files.
outputRDataMerge: Character. Output directory for merged RData files.
sexColumn: Character. Sex column name.
outputLogs: Character. Directory for log files.
outputDir: Character. Base output directory.

Value

Invisibly returns NULL. This function is called for its side effects, preparing analysis-ready phenotype-methylation datasets by subsetting, merging timepoints, aligning samples with beta, M, and CN matrices, and writing processed phenotype tables and RData objects to disk.

Examples

tmp <- tempdir()
stopifnot(dir.exists(tmp))

# \donttest{
preprocessingPheno(
  phenoFile = "data/preprocessingMinfiEwasWater/phenoLC.csv",
  sepType = "",
  betaPath = "rData/preprocessingMinfiEwasWater/metrics/beta_NomFilt_MSetF_Flt_Rxy_Ds_Rc.RData",
  mPath = "rData/preprocessingMinfiEwasWater/metrics/m_NomFilt_MSetF_Flt_Rxy_Ds_Rc.RData",
  cnPath = "rData/preprocessingMinfiEwasWater/metrics/cn_NomFilt_MSetF_Flt_Rxy_Ds_Rc.RData",
  SampleID = "Sample_Name",
  timeVar = "Timepoint",
  timepoints = "1,2",
  combineTimepoints = "1,2",
  outputPheno = "data/preprocessingPheno",
  outputRData = "rData/preprocessingPheno/metrics",
  outputRDataMerge = "rData/preprocessingPheno/mergeData",
  sexColumn = "Sex",
  outputLogs = "logs",
  outputDir = "data/preprocessingPheno"
)
#> ==== Starting Phenotype Preprocessing ====
#> Start Time:                2026-04-02 05:15:45 
#> Log file path:             logs/log_preprocessingPheno.txt 
#> 
#> Phenotype file:            data/preprocessingMinfiEwasWater/phenoLC.csv 
#> Beta path:                 rData/preprocessingMinfiEwasWater/metrics/beta_NomFilt_MSetF_Flt_Rxy_Ds_Rc.RData 
#> M-values path:             rData/preprocessingMinfiEwasWater/metrics/m_NomFilt_MSetF_Flt_Rxy_Ds_Rc.RData 
#> CN path:                   rData/preprocessingMinfiEwasWater/metrics/cn_NomFilt_MSetF_Flt_Rxy_Ds_Rc.RData 
#> 
#> Identifier column:         Sample_Name 
#> Timepoint column:         Timepoint 
#> Timepoints (if present):   1,2 
#> Combine timepoints:        1,2 
#> 
#> Sex column:                Sex 
#> Output phenotype dir:      data/preprocessingPheno 
#> RData metrics dir:         rData/preprocessingPheno/metrics 
#> RData merge dir:           rData/preprocessingPheno/mergeData 
#> 
#> =======================================================================
#> Warning: cannot open compressed file 'rData/preprocessingMinfiEwasWater/metrics/beta_NomFilt_MSetF_Flt_Rxy_Ds_Rc.RData', probable reason 'No such file or directory'
#> Error in readChar(con, 5L, useBytes = TRUE): cannot open the connection
# }