From f94a879fad391a01df1d09798cf7837f83b7b82e Mon Sep 17 00:00:00 2001
From: ClarissaFeuersteinAkgoz
 <48914703+ClarissaFeuersteinAkgoz@users.noreply.github.com>
Date: Tue, 2 Jun 2020 20:17:20 +0200
Subject: [PATCH 1/4] trial :(

---
 .gitignore | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 46b6fe1..f0929d0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,5 @@
 Meta
-.DS_Store
+.DS_Store 
 .Rproj.user
 .Rproj
 .Rhistory

From 903deba06cb3c60f35b3589260a4f737d3ac6117 Mon Sep 17 00:00:00 2001
From: ClarissaFeuersteinAkgoz
 <48914703+ClarissaFeuersteinAkgoz@users.noreply.github.com>
Date: Thu, 3 Jun 2021 22:07:15 +0200
Subject: [PATCH 2/4] Update methrix_operations.R

Function to calculate hydroxymethylation proportions from BS and oxBS data
returns a methrix object with proportions for
mC (~oxBS)
hmC
C
mC+hmC (~BS)

dependencies to add?: MLML2R, rlist,
manuall is still missing
---
 R/methrix_operations.R | 80 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 80 insertions(+)

diff --git a/R/methrix_operations.R b/R/methrix_operations.R
index ea84464..0e4e4b6 100644
--- a/R/methrix_operations.R
+++ b/R/methrix_operations.R
@@ -871,3 +871,83 @@ convert_methrix <- function(m = NULL) {
         desc = metadata(m)$descriptive_stats)
     return(m)
 }
+
+#--------------------------------------------------------------------------------------------------------------------------
+#' Calculates hydroxymethylation from BS and oxBS data
+#' @details Takes a \code{\link{methrix}} object and returns with the same object with delayed array assay slots
+#' @param m An object of class \code{\link{methrix}}
+#' @return An object of class \code{\link{methrix}}
+calculate_proportions<- function (m){
+  
+  # check if input data set is ok
+  # for each "Sample_ID" there must be a oxBS and BS data set, defined in "Sequencing_type"
+  anno <- data.frame(colData(m))
+  anno <- as.data.frame(lapply(anno, factor))
+  for(i in levels(anno$Sample_ID)){
+    anno_sub <- anno[anno$Sample_ID==i,]
+    print(i)
+    if (nrow(anno_sub)!=2 | sum(is.element(c("oxBS", "BS"), anno_sub$Sequencing_type))!=2 )
+    {    stop("oxBS or BS sample is missing or in excess for a sample type.",
+              call. = T)
+    }
+  } 
+  
+  # extract data for MLML2R
+  methylation <- get_matrix(m, type = 'M')
+  covarage <- get_matrix(m, type = 'C')
+  
+  
+  id_BS <- which(colData(m)$Sequencing_type=="BS")
+  id_oxBS <- which(colData(m)$Sequencing_type=="oxBS")
+  
+  #match samples of BS and oxBS to same order
+  id_oxBS <- id_oxBS[match(colData(m)$Sample_ID[id_BS], colData(m)$Sample_ID[id_oxBS])]
+  
+  colData(m)$Sample_ID[id_BS]==colData(m)$Sample_ID[id_oxBS]
+  
+  
+  #total count
+  TotalBS <- covarage[,id_BS]
+  TotalOxBS <- covarage[,id_oxBS]
+  
+  #methylation count
+  C_BS <- data.frame(methylation[,id_BS])*data.frame(covarage[,id_BS])
+  C_OxBS<- data.frame(methylation[,id_oxBS])*data.frame(covarage[,id_oxBS])
+  
+  #unmethylation count
+  T_BS<- data.frame(TotalBS) - data.frame(C_BS)
+  T_OxBS<- data.frame(TotalOxBS) - data.frame(C_OxBS)
+  
+  Tm = as.matrix(C_BS)
+  Um = as.matrix(T_BS)
+  Lm = as.matrix(T_OxBS)
+  Mm = as.matrix(C_OxBS)
+  
+  results_exact <- MLML2R::MLML(T.matrix = Tm, 
+                                U.matrix = Um, 
+                                L.matrix = Lm, 
+                                M.matrix = Mm)
+  
+  
+  #create new methrix object
+  
+  # get the lowest covarage among both sequencing types
+  
+  min_cov <- rlist::list.cbind(lapply(1:length(id_BS), function(x) rowMins(covarage[,c(id_BS[x],id_oxBS[x])])))
+  
+  #prepare methrix dataset for mC, hmC and C data
+  m_MLML2R <- m[,c(id_BS,id_BS,id_BS,id_BS)]
+  m_MLML2R@colData$Sequencing_type <- NULL
+  m_MLML2R@colData$Mark <-c(rep("mC",length(id_BS)),rep("hmC",length(id_BS)),rep("C",length(id_BS)),rep("mChmC",length(id_BS))) 
+  mChmC<- as.matrix(results_exact$mC)+as.matrix(results_exact$hmC)
+  m_MLML2R@ assays@ data@ listData$ beta <- cbind(results_exact$mC,results_exact$hmC,results_exact$C,mChmC)
+  m_MLML2R@ assays@ data@ listData$ cov <-  cbind(min_cov,min_cov,min_cov,min_cov)
+  
+  #change names in methrix object
+  names <- gsub("bs", "",m_MLML2R@colData@ listData$ Sample_Name)
+  m_MLML2R <-replace_names(m_MLML2R,paste0(names, m_MLML2R@colData$Mark))
+  
+  return(m_MLML2R)
+  
+}
+

From 2342b52efa62f133f2746154d8ccc0d55f847fac Mon Sep 17 00:00:00 2001
From: ClarissaFeuersteinAkgoz
 <48914703+ClarissaFeuersteinAkgoz@users.noreply.github.com>
Date: Thu, 3 Jun 2021 23:35:01 +0200
Subject: [PATCH 3/4] Update accessory_funcs.R

function needed when calculating hmC from oxBS and BS
---
 R/accessory_funcs.R | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/R/accessory_funcs.R b/R/accessory_funcs.R
index e7eced1..a93d579 100644
--- a/R/accessory_funcs.R
+++ b/R/accessory_funcs.R
@@ -612,3 +612,14 @@ get_y_lims <- function(vec) {
   
   list(y_lims = y_lims, y_at = y_at)
 }
+
+                                                                   
+#--------------------------------------------------------------------------------------------------------------------------
+# function to replace names when working with oxBS and BS data
+replace_names = function(m, value) {
+  colData(m)$rownames = value
+  colnames(assays(m)$beta) = value
+  colnames(assays(m)$cov) = value
+  colData(m)$Sample_Name = value
+  return(m)
+} 

From 0db7e75f692e04c61bcd7a660a7687cdcc1443ef Mon Sep 17 00:00:00 2001
From: ClarissaFeuersteinAkgoz
 <48914703+ClarissaFeuersteinAkgoz@users.noreply.github.com>
Date: Thu, 3 Jun 2021 23:40:52 +0200
Subject: [PATCH 4/4] Update methrix_operations.R

use of accessor functions
---
 R/methrix_operations.R | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/R/methrix_operations.R b/R/methrix_operations.R
index 0e4e4b6..8954e68 100644
--- a/R/methrix_operations.R
+++ b/R/methrix_operations.R
@@ -937,15 +937,17 @@ calculate_proportions<- function (m){
   
   #prepare methrix dataset for mC, hmC and C data
   m_MLML2R <- m[,c(id_BS,id_BS,id_BS,id_BS)]
-  m_MLML2R@colData$Sequencing_type <- NULL
-  m_MLML2R@colData$Mark <-c(rep("mC",length(id_BS)),rep("hmC",length(id_BS)),rep("C",length(id_BS)),rep("mChmC",length(id_BS))) 
+  colData(m_MLML2R)$Sequencing_type <- NULL
+  colData(m_MLML2R)$Mark <-c(rep("mC",length(id_BS)),rep("hmC",length(id_BS)),rep("C",length(id_BS)),rep("mChmC",length(id_BS))) 
   mChmC<- as.matrix(results_exact$mC)+as.matrix(results_exact$hmC)
-  m_MLML2R@ assays@ data@ listData$ beta <- cbind(results_exact$mC,results_exact$hmC,results_exact$C,mChmC)
-  m_MLML2R@ assays@ data@ listData$ cov <-  cbind(min_cov,min_cov,min_cov,min_cov)
-  
+  assays(m_MLML2R)$beta <- cbind(results_exact$mC,results_exact$hmC,results_exact$C,mChmC)
+  min_cov_mat <- cbind(min_cov,min_cov,min_cov,min_cov)
+  colnames(min_cov_mat) <- colnames(assays(m_MLML2R)$cov)
+  assays(m_MLML2R)$cov  <-  min_cov_mat  
+                                      
   #change names in methrix object
-  names <- gsub("bs", "",m_MLML2R@colData@ listData$ Sample_Name)
-  m_MLML2R <-replace_names(m_MLML2R,paste0(names, m_MLML2R@colData$Mark))
+  names <- gsub("bs", "", colData(m_MLML2R)$Sample_Name)
+  m_MLML2R <-replace_names(m_MLML2R,paste0(names, colData(m_MLML2R)$Mark))
   
   return(m_MLML2R)