From 77522f640e4d555c2d0ab26d74f70f8bc983017f Mon Sep 17 00:00:00 2001
From: gabrielodom <gabriel.odom@fiu.edu>
Date: Tue, 29 Mar 2022 17:07:39 -0400
Subject: [PATCH] Making progress on Issue #14; also related to Issue #18 and
 Issue #19

---
 R/lmmTest.R           | 41 +++++++++++++++++++++++----------------
 R/lmmTestAllRegions.R | 45 +++++++++++++++++++++++++++----------------
 2 files changed, 52 insertions(+), 34 deletions(-)

diff --git a/R/lmmTest.R b/R/lmmTest.R
index 00c04d5..d319ca8 100644
--- a/R/lmmTest.R
+++ b/R/lmmTest.R
@@ -80,11 +80,13 @@ lmmTest <- function(betaOne_df, pheno_df, contPheno_char, covariates_char,
                     outLogFile = NULL){
   # browser()
 
+  ###  Inputs  ###
   modelType <- match.arg(modelType)
   arrayType <- match.arg(arrayType)
   genome <- match.arg(genome)
 
-  ### Transpose betaOne_df from wide to long ###
+  
+  ###  Wrangle  ###
   betaOne_df$ProbeID <- row.names(betaOne_df)
   betaOneTransp_df <- reshape(
     betaOne_df,
@@ -95,15 +97,16 @@ lmmTest <- function(betaOne_df, pheno_df, contPheno_char, covariates_char,
     timevar = "Sample"
   )
 
-  ### Calculate M values ###
+  # Calculate M values
   betaOneTransp_df$Mvalue <- log2(
     betaOneTransp_df$beta / (1 - betaOneTransp_df$beta)
   )
 
-  ### Merge transposed beta matrix with phenotype ###
+  # Merge transposed beta matrix with phenotype
   betaOnePheno_df <- merge(betaOneTransp_df, pheno_df, by = "Sample")
 
-  # regionNames
+  
+  ###  Setup  ###
   regionName <- NameRegion(
     OrderCpGsByLocation(
       CpGs_char = betaOne_df$ProbeID,
@@ -114,17 +117,22 @@ lmmTest <- function(betaOne_df, pheno_df, contPheno_char, covariates_char,
       output = "dataframe"
     )
   )
-
-  modelFormula_char <- .MakeLmmFormula(
-    contPheno_char, covariates_char, modelType
-  )
-
+  
   if(!is.null(outLogFile)){
     cat(paste0("Analyzing region ", regionName, ". \n"))
   } else {
     message("Analyzing region ", regionName, ". \n")
   }
 
+  modelFormula_char <- .MakeLmmFormula(
+    contPheno_char = contPheno_char,
+    covariates_char = covariates_char,
+    modelType = modelType
+  )
+
+  
+  ###  Analysis  ###
+  # Run
   f <- tryCatch(
     {
       suppressMessages(
@@ -134,7 +142,7 @@ lmmTest <- function(betaOne_df, pheno_df, contPheno_char, covariates_char,
     error = function(e){NULL}
   )
 
-
+  # Check
   if(is.null(f)){
 
     ps_df <- data.frame(
@@ -170,22 +178,21 @@ lmmTest <- function(betaOne_df, pheno_df, contPheno_char, covariates_char,
 
   }
 
-  ### split regionName into chrom, start, end
+  
+  ###  Return  ###
+  # split regionName into chrom, start, end
   chrom <- sub(":.*",    "", regionName)
   range <- sub("c.*:",   "", regionName)
   start <- sub("-\\d*",  "", range)
   end   <- sub("\\d*.-", "", range)
 
-  ### Return results ###
+  # results
   nCpGs <- nrow(betaOne_df)
-  result <- cbind(
-    chrom, start, end, nCpGs,
-    ps_df,
+  cbind(
+    chrom, start, end, nCpGs, ps_df,
     stringsAsFactors = FALSE
   )
 
-  result
-
 }
 
 
diff --git a/R/lmmTestAllRegions.R b/R/lmmTestAllRegions.R
index 516171d..b593b46 100644
--- a/R/lmmTestAllRegions.R
+++ b/R/lmmTestAllRegions.R
@@ -119,14 +119,22 @@ lmmTestAllRegions <- function(
   nCores_int = 1L,
   ...){
   # browser()
-
-  warnLvl <- options()$warn
-  options(warn = 1)
-
-  ###  Setup  ###
+  
+  
+  ###  Inputs  ###
   modelType <- match.arg(modelType)
-  arrayType <- match.arg(arrayType)
+  
+  # Available manifest files are: 
+  #   "EPIC.hg19.manifest"  "EPIC.hg38.manifest"
+  #   "HM450.hg19.manifest" "HM450.hg38.manifest"
   genome <- match.arg(genome)
+  arrayType <- match.arg(arrayType)
+  manifest <- paste(
+    switch(arrayType, "450k" = "HM450", "EPIC" = "EPIC"),
+    genome, "manifest",
+    sep = "."
+  )
+  CpGlocations.gr <- ImportSesameData(manifest)  
 
   if (is(betas, "matrix")){
     beta_df <- as.data.frame(betas)
@@ -141,6 +149,11 @@ lmmTestAllRegions <- function(
 
   CpGnames <- rownames(beta_df)
 
+  
+  ###  Setup Log File  ###
+  warnLvl <- options()$warn
+  options(warn = 1)
+  
   writeLog_logi <- !is.null(outLogFile)
   if(writeLog_logi){
 
@@ -158,13 +171,14 @@ lmmTestAllRegions <- function(
   }
 
 
-  ###  Split Data by Region  ###
+  ###  Run mixed model for all the contiguous comethylated regions  ###
+  # Split Data by Region
   coMethBetaDF_ls <- lapply(
     region_ls,
     function(x) beta_df[which(CpGnames %in% x), ]
   )
-
-  ###  Run mixed model for all the contiguous comethylated regions  ###
+  
+  # Apply
   cluster <- CreateParallelWorkers(nCores_int, ...)
 
   results_ls <- bplapply(
@@ -177,11 +191,14 @@ lmmTestAllRegions <- function(
     modelType,
     genome,
     arrayType,
-    manifest_gr = NULL,
+    manifest_gr = CpGlocations.gr,
     ignoreStrand,
     outLogFile
   )
 
+  
+  ###  Close Log File  ###
+  options(warn = warnLvl)
   if(writeLog_logi){
 
     cat("\n")
@@ -210,8 +227,7 @@ lmmTestAllRegions <- function(
   }
 
 
-
-  ### Output results ###
+  ###  Output results  ###
   if (length(results_ls) > 0){
 
     outDF <- do.call(rbind, results_ls)
@@ -220,13 +236,8 @@ lmmTestAllRegions <- function(
 
   }
 
-
-  options(warn = warnLvl)
-
   if (is.null(outFile)){
-
     outDF
-
   } else {
 
     message("writing results to ", outFile,".csv")