Run methylationGLMM_T1T2.R
methylationGLMM_T1T2(
inputPheno = "rData/preprocessingPheno/mergeData/phenoBetaT1T2.RData",
outputLogs = "logs/",
outputRData = "rData/methylationGLMM_T1T2/models",
outputPlots = "figures/methylationGLMM_T1T2",
personVar = "person",
timeVar = "Timepoint",
phenotypes =
"DASS_Depression,DASS_Anxiety,DASS_Stress,PCL5_TotalScore,\n MHCSF_TotalScore,BRS_TotalScore",
covariates = "Sex,Age,Ethnicity,TraumaDefinition,Leukocytes,Epithelial.cells",
factorVars = "Sex,Ethnicity,TraumaDefinition,Timepoint",
lmeLibs = "lme4,lmerTest",
prsMap = NULL,
libPath = NULL,
cpgPrefix = "cg",
cpgLimit = NA,
nCores = 32,
summaryPval = NA,
plotWidth = 2000,
plotHeight = 1000,
plotDPI = 150,
interactionTerm = NULL,
saveSignificantInteractions = TRUE,
significantInteractionDir = "preliminaryResults/cpgs/methylationGLMM_T1T2",
significantInteractionPval = 0.05,
saveTxtSummaries = TRUE,
chunkSize = NULL,
summaryTxtDir = "preliminaryResults/summary/methylationGLMM_T1T2/lmer",
fdrThreshold = 0.05,
padjmethod = "fdr",
annotationPackage = "IlluminaHumanMethylationEPICv2anno.20a1.hg38",
annotationCols =
"Name,chr,pos,UCSC_RefGene_Group,UCSC_RefGene_Name,\n Relation_to_Island,GencodeV41_Group",
annotatedLMEOut = "data/methylationGLMM_T1T2"
)Character. Path to merged longitudinal phenotype and beta-value RData file.
Character. Directory for log files.
Character. Directory for model RData outputs.
Character. Directory for output plots.
Character. Subject identifier variable.
Character. Time variable name.
Character. Comma-separated phenotype variables to model.
Character. Comma-separated covariate variables.
Character. Comma-separated factor variables.
Character. Mixed-effects modelling libraries.
Character or NULL. Optional PRS mapping file.
Character or NULL. Optional library path.
Character. CpG identifier prefix.
Integer or NA. Maximum number of CpGs to analyse.
Integer. Number of CPU cores to use.
Numeric or NA. P-value threshold for summaries.
Integer. Plot width in pixels.
Integer. Plot height in pixels.
Integer. Plot resolution in DPI.
Character or NULL. Optional interaction term.
Logical. Save significant interaction results.
Character. Directory for significant interactions.
Numeric. P-value threshold for significant interactions.
Logical. Save text summaries.
Integer. Number of CpGs processed per chunk.
Character. Directory for summary text files.
Numeric. FDR threshold.
Character. P-value adjustment method.
Character. Annotation package name.
Character. Annotation columns to extract.
Character. Output directory for annotated results.
Invisibly returns NULL. This function is called for its side effects,
running CpG-level longitudinal mixed-effects models and writing model
results, interaction summaries, plots, and annotated tables to disk.
tmp <- tempdir()
stopifnot(dir.exists(tmp))
# \donttest{
methylationGLMM_T1T2(
inputPheno = "rData/preprocessingPheno/mergeData/phenoBetaT1T2.RData",
outputLogs = "logs",
outputRData = "rData/methylationGLMM_T1T2/models",
outputPlots = "figures/methylationGLMM_T1T2",
personVar = "person",
timeVar = "Timepoint",
phenotypes = "DASS_Depression,DASS_Anxiety,DASS_Stress,
PCL5_TotalScore,MHCSF_TotalScore,BRS_TotalScore",
covariates = "Sex,Age,Ethnicity,TraumaDefinition,
Leukocytes,Epithelial.cells",
factorVars = "Sex,Ethnicity,TraumaDefinition,Timepoint",
lmeLibs = "lme4,lmerTest",
prsMap = NULL,
libPath = NULL,
cpgPrefix = "cg",
cpgLimit = NA,
nCores = 4,
summaryPval = NA,
plotWidth = 2000,
plotHeight = 1000,
plotDPI = 150,
interactionTerm = "TreatvControl_Time1_vs_Time2",
saveSignificantInteractions = TRUE,
significantInteractionDir =
"preliminaryResults/cpgs/methylationGLMM_T1T2",
significantInteractionPval = 0.05,
saveTxtSummaries = TRUE,
chunkSize = 10000,
summaryTxtDir =
"preliminaryResults/summary/methylationGLMM_T1T2/lmer",
fdrThreshold = 0.05,
padjmethod = "fdr",
annotationPackage =
"IlluminaHumanMethylationEPICv2anno.20a1.hg38",
annotationCols =
"Name,chr,pos,UCSC_RefGene_Group,
UCSC_RefGene_Name,Relation_to_Island,
GencodeV41_Group",
annotatedLMEOut = "data/methylationGLMM_T1T2"
)
#> ==== Starting DNAm LME Analysis (Timepoint 1 vs 3) ====
#> Start time: 2026-04-02 05:15:45
#> Input phenotype + beta file: rData/preprocessingPheno/mergeData/phenoBetaT1T2.RData
#> Person ID variable: person
#> Timepoint variable: Timepoint
#> Phenotypes: DASS_Depression,DASS_Anxiety,DASS_Stress,
#> PCL5_TotalScore,MHCSF_TotalScore,BRS_TotalScore
#> Covariates: Sex,Age,Ethnicity,TraumaDefinition,
#> Leukocytes,Epithelial.cells
#> PRS mapping: None
#> Factor variables: Sex,Ethnicity,TraumaDefinition,Timepoint
#> LME libraries: lme4,lmerTest
#> Library path: /__w/_temp/Library
#> CpG prefix pattern: cg
#> CpG limit: All CpGs
#> Number of cores: 4
#> Interaction term: TreatvControl_Time1_vs_Time2
#> Save significant interactions: TRUE
#> Significant interaction p-value cutoff: 0.05
#> Directory to save significant interactions: preliminaryResults/cpgs/methylationGLMM_T1T2
#> Save summary TXT files: TRUE
#> Chunk size for processing CpGs: 10000
#> Summary p-value threshold: NA
#> Padjmethod: fdr
#> FDR threshold for significance: 0.05
#> Multiple testing correction method: fdr
#> Save significant interaction CpGs: TRUE
#> Significant interaction p-value cutoff: 0.05
#> Directory to save significant interaction CpGs: preliminaryResults/cpgs/methylationGLMM_T1T2
#> Summary TXT output directory: preliminaryResults/summary/methylationGLMM_T1T2/lmer
#> Annotation package: IlluminaHumanMethylationEPICv2anno.20a1.hg38
#> Annotation columns: Name,chr,pos,UCSC_RefGene_Group,
#> UCSC_RefGene_Name,Relation_to_Island,
#> GencodeV41_Group
#> FDR threshold for significance: 0.05
#> Output logs directory: logs
#> Directory to save annotated LME results: data/methylationGLMM_T1T2
#> =======================================================================
#>
#> Loading input phenotype + beta file...
#> Warning: cannot open compressed file 'rData/preprocessingPheno/mergeData/phenoBetaT1T2.RData', probable reason 'No such file or directory'
#> Error in readChar(con, 5L, useBytes = TRUE): cannot open the connection
# }