Changed input format

DESCRIPTION

@@ -31,4 +31,4 @@ Remotes:
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1

NAMESPACE

@@ -4,6 +4,7 @@ export(compare_results)
 export(deconvolute)
 export(deconvolution_methods)
 export(normalize_deconv_results)
+export(run_all_methods)
 export(run_epidish)
 export(run_flowsortedblood)
 export(run_methylcc)

R/FlowSortedBlood.R

@@ -1,7 +1,6 @@
 #' Run the improved Houseman method
 #'
-#' @param meth methylated data matrix
-#' @param unmeth unmethylated data matrix
+#' @param methyl_set A minfi MethylSet
 #' @param array type of methylation array that was used. possible options are '450k' and 'EPIC'
 #' @param compositeCellType Which composite cell type is being deconvoluted. Should be one of "Blood", "CordBloodCombined", "CordBlood", "CordBloodNorway", "CordTissueAndBlood", or "DLPFC". See details for preferred approaches.
 #' @param processMethod Joint normalization/background correction for user and reference data. For MethylSet objects only "preprocessQuantile" is available. Set it to any minfi preprocessing function as a character if you want to override it, like "preprocessFunnorm"
@@ -21,15 +20,14 @@
 #' @export
 #'
 #' @examples
-run_flowsortedblood <- function(meth, unmeth, array = c('450k','EPIC'),
+run_flowsortedblood <- function(methyl_set, array = c('450k','EPIC'),
                                 compositeCellType=c('Blood','CordBloodCombined','CordBlood','CordBloodNorway','CordTissueAndBlood','DLPFC'),
                                 processMethod = 'preprocessQuantile', probeSelect = c('IDOL','both','any'), cellTypes =c('CD8T','CD4T','NK','Bcell','Mono','Neu'),
                                 referencePlatform = c('IlluminaHumanMethylationEPIC','IlluminaHumanMethylation450k','IlluminaHumanMethylation27k'),
                                 referenceset = NULL, CustomCpGs = NULL, meanPlot = FALSE, verbose = TRUE, lessThanOne = FALSE, cellCounts = NULL, ...){
   require(FlowSorted.Blood.EPIC)
 
-  check_input(meth, unmeth)
-  methyl_set <- minfi::MethylSet(Meth = meth, Unmeth = unmeth)
+  check_input_mset(methyl_set)
 
   if (length(array) > 1) {
     array <- array[1]

R/epidish.R

@@ -1,7 +1,6 @@
 #' run EpiDISH
 #'
-#' @param meth methylated data matrix
-#' @param unmeth unmethylated data matrix
+#' @param methyl_set A minfi MethylSet
 #' @param mode Choice of a reference-based method ('RPC','CBS','CP')
 #' @param reference A matrix of reference 'centroids', i.e. representative molecular profiles, 
 #' for a number of cell subtypes. rows label molecular features (e.g. CpGs,...) 
@@ -39,14 +38,14 @@
 #' @export
 #'
 #' @examples
-run_epidish <- function(meth, unmeth, mode=c('RPC', 'CBS', 'CP'), 
+run_epidish <- function(methyl_set, mode=c('RPC', 'CBS', 'CP'), 
                         reference=c('blood','breast','epithelial'), 
                         maxit = 50, nu.v = c(0.25, 0.5, 0.7), 
                         constraint = c("inequality", "equality")){
   require(EpiDISH)
 
-  check_input(meth, unmeth)
-  beta_matrix <- create_beta(meth, unmeth)
+  check_input_mset(methyl_set)
+  beta_matrix <- minfi::getBeta(methyl_set)
 
   if (length(mode) > 1) {
     mode <- mode[1]

R/main.R

@@ -15,8 +15,7 @@ deconvolution_methods <- c(
 
 #' Deconvolution
 #'
-#' @param meth methylated data matrix
-#' @param unmeth unmethylated data matrix 
+#' @param methyl_set A minfi MethylSet
 #' @param method A string specifying the method. Supported methods are 'epidish', 'flowsorted', 'methylcc', 'methylresolver'
 #' @param normalize_results   Whether the deconvolution results should be normalized.
 #'   Negative values will be put to 0, and the estimates will be normalized to sum to 1.
@@ -30,11 +29,9 @@ deconvolution_methods <- c(
 #' @examples 
 #' 
 #' ex_data <- minfiData::MsetEx
-#' meth <- minfi::getMeth(ex_data)
-#' unmeth <- minfi::getUnmeth(ex_data)
 #' 
-#' result <- deconvolute(meth, unmeth, method='epidish')
-deconvolute <- function(meth, unmeth, method=deconvolution_methods, normalize_results = FALSE, ...){
+#' result <- deconvolute(ex_data, method='epidish')
+deconvolute <- function(methyl_set, method=deconvolution_methods, normalize_results = FALSE, ...){
 
   if (length(method) > 1) {
     stop(
@@ -51,10 +48,10 @@ deconvolute <- function(meth, unmeth, method=deconvolution_methods, normalize_re
 
 
   result <- switch (method,
-    epidish = run_epidish(meth, unmeth, ...)$estF,
-    flowsorted = run_flowsortedblood(meth, unmeth, ...)$prop,
-    methylcc = run_methylcc(meth, unmeth, ...),
-    methylresolver = run_methylresolver(meth, unmeth, ...)$result_fractions
+    epidish = run_epidish(methyl_set, ...)$estF,
+    flowsorted = run_flowsortedblood(methyl_set, ...)$prop,
+    methylcc = as.matrix(run_methylcc(methyl_set, ...)),
+    methylresolver = as.matrix(run_methylresolver(methyl_set, ...)$result_fractions)
   )
 
   if(!is.null(result)){
@@ -79,12 +76,12 @@ deconvolute <- function(meth, unmeth, method=deconvolution_methods, normalize_re
 #' @export
 #'
 #' @examples
-run_all_methods <- function(meth, unmeth, array = c('450k','EPIC')){
+run_all_methods <- function(methyl_set, array = c('450k','EPIC')){
 
-  res_epidish <- run_epidish(meth, unmeth)
-  res_flowsorted <- run_flowsortedblood(meth, unmeth, array = array)
-  res_methylcc <- run_methylcc(meth, unmeth, array = array)
-  res_methylresolver <- run_methylresolver(meth, unmeth)
+  res_epidish <- run_epidish(methyl_set)
+  res_flowsorted <- run_flowsortedblood(methyl_set, array = array)
+  res_methylcc <- run_methylcc(methyl_set, array = array)
+  res_methylresolver <- run_methylresolver(methyl_set)
   results <- list(res_epidish$estF, res_flowsorted$prop, res_methylcc, res_methylresolver$result_fractions)
   names(results) <- c('EpiDISH','FlowSorted','MethylCC','MethylResolver')
 

R/methylResolver.R

@@ -1,7 +1,6 @@
 #' Run MethylResolver
 #'
-#' @param meth methylated data matrix
-#' @param unmeth unmethylated data matrix 
+#' @param methyl_set A minfi MethylSet
 #' @param doPar Whether to use parallel processing to speed up the deconvolution computation if many samples are present. Default is FALSE. 
 #' @param numCores Number of cores used for parallel processing to speed up the deconvolution of many samples. Requires doPar = TRUE. Default is 1. numCores = "auto" is max number of cores available minus one. 
 #' @param alpha Set the alpha parameter for LTS deconvolution. This is the fraction of optimal CpGs from the signature matrix which are used for deconvolution. Must be between 0 and 1. Users can specify a vector or a single number. If a vector is specified, a grid search of the values is conducted and the alpha value that results in the lowest RMSE between the original and reconstructed mixture is selected. Default is seq(0.5,0.9,by = 0.05). 
@@ -13,15 +12,20 @@
 #' @export
 #'
 #' @examples
-run_methylresolver <- function(meth, unmeth, doPar = F, numCores = 1, alpha = seq(0.5,0.9,by = 0.05),
+run_methylresolver <- function(methyl_set, doPar = F, numCores = 1, alpha = seq(0.5,0.9,by = 0.05),
                                absolute = TRUE, purityModel = MethylResolver::RFmodel, seed = 1){
 
   require(MethylResolver)
 
   set.seed(seed)
 
-  check_input(meth, unmeth)
-  beta_matrix <- create_beta(meth, unmeth)
+  check_input_mset(methyl_set) 
+  beta_matrix <- minfi::getBeta(methyl_set)
+
+  if (length(alpha) > 1){
+    warning("MethylResolver may fail if multiple alpha values are provided. If this occurs, specify a single alpha value between 0.5 and 1.",
+            immediate. = TRUE)
+  }
 
   result_methylresolver <- MethylResolver::MethylResolver(methylMix = beta_matrix, 
                                                           methylSig = MethylResolver::MethylSig, 

R/methylcc.R

@@ -1,7 +1,6 @@
 #' run methylCC deconvolution
 #'
-#' @param meth methylated data matrix
-#' @param unmeth unmethylated data matrix
+#' @param methyl_set A minfi MethylSet
 #' @param array type of methylation array that was used. possible options are '450k' and 'EPIC'
 #' @param find_dmrs_object If the user would like to supply different differentially methylated regions, they can use the output from the find_dmrs function to supply different regions to estimatecc.
 #' @param verbose TRUE/FALSE argument specifying if verbose messages should be returned or not. Default is TRUE.
@@ -23,7 +22,7 @@
 #' @export
 #'
 #' @examples
-run_methylcc <- function(meth, unmeth, array = c('450k','EPIC'),
+run_methylcc <- function(methyl_set, array = c('450k','EPIC'),
                          find_dmrs_object = NULL, verbose = TRUE,
                          epsilon = 0.01, max_iter = 100, take_intersection = FALSE,
                          include_cpgs = FALSE, include_dmrs = TRUE,
@@ -37,8 +36,7 @@ run_methylcc <- function(meth, unmeth, array = c('450k','EPIC'),
 
   set.seed(seed)
 
-  check_input(meth, unmeth)
-  methyl_set <- minfi::MethylSet(Meth = meth, Unmeth = unmeth)
+  check_input_mset(methyl_set)
 
   if (length(array) > 1) {
     array <- array[1]

R/util.R

@@ -17,6 +17,21 @@ check_input <- function(meth, unmeth){
   }
 }
 
+#' Check input methylSet
+#'
+#' @param methyl_set
+#'
+#'
+#' @examples
+check_input_mset <- function(methyl_set){
+  if(!is(methyl_set, "MethylSet")){
+    stop('Input is not a MethylSet, stopping.')
+  }
+  if(all(is.na(methyl_set))){
+    stop('All entries in the MethylSet are NA, stopping.')
+  }
+}
+
 
 #' Create beta matrix from meth and unmeth matrices
 #'

tests/testthat/test_methods.R

@@ -9,8 +9,7 @@ unmeth <- minfi::getUnmeth(ex_data)
 # write.csv()
 
 test_that("EpiDISH works", {
-  epidish_res <- methylDeconv::run_epidish(meth = meth, 
-                                           unmeth = unmeth)$estF
+  epidish_res <- methylDeconv::run_epidish(methyl_set = ex_data)$estF
   check_result <- as.matrix(read.csv("test_results/epidish.csv",
                                      row.names = 1,
                                      check.names = FALSE
@@ -23,8 +22,7 @@ test_that("EpiDISH works", {
 
 
 test_that("methylCC works", {
-  methylcc_res <- as.matrix(methylDeconv::run_methylcc(meth = meth, 
-                                                       unmeth = unmeth))
+  methylcc_res <- as.matrix(methylDeconv::run_methylcc(methyl_set = ex_data))
   check_result <- as.matrix(read.csv("test_results/methylcc.csv",
                                      row.names = 1,
                                      check.names = FALSE
@@ -36,8 +34,7 @@ test_that("methylCC works", {
 })
 
 test_that("FlowSorted works", {
-  flowSorted_res <- methylDeconv::run_flowsortedblood(meth = meth, 
-                                                      unmeth = unmeth)$prop
+  flowSorted_res <- methylDeconv::run_flowsortedblood(methyl_set = ex_data)$prop
   check_result <- as.matrix(read.csv("test_results/flowsorted.csv",
                                      row.names = 1,
                                      check.names = FALSE
@@ -49,8 +46,7 @@ test_that("FlowSorted works", {
 })
 
 test_that("MethylResolver works", {
-  methylResolver_res <- methylDeconv::run_methylresolver(meth = meth, 
-                                                         unmeth = unmeth)$result_fractions
+  methylResolver_res <- as.matrix(methylDeconv::run_methylresolver(methyl_set = ex_data, alpha = 1)$result_fractions)
   check_result <- as.matrix(read.csv("test_results/methylresolver.csv",
                                      row.names = 1,
                                      check.names = FALSE