finalize meth atlas

omnideconv · Nov 21, 2024 · 3f1b7f7 · 3f1b7f7
1 parent 9593ff4
commit 3f1b7f7
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Showing 8 changed files with 21 additions and 21 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -17,7 +17,13 @@ Imports:
     FlowSorted.Blood.EPIC,
     ggplot2,
     methylCC,
-    minfi
+    minfi,
+    reticulate,
+    MethylResolver,
+    data.table,
+    dplyr,
+    reshape,
+    tibble
 Suggests: 
     Biobase,
     FlowSorted.Blood.450k,
@@ -27,7 +33,8 @@ Suggests:
     IlluminaHumanMethylation450kmanifest,
     testthat (>= 3.0.0),
     knitr,
-    rmarkdown
+    rmarkdown,
+    minfiData
 Remotes:
     omnideconv/MethylResolver
 Config/testthat/edition: 3

diff --git a/R/FlowSortedBlood.R b/R/FlowSortedBlood.R
@@ -25,8 +25,7 @@ run_flowsortedblood <- function(methyl_set, array = c('450k','EPIC'),
                                 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_mset(methyl_set)
 
   if (length(array) > 1) {

diff --git a/R/epidish.R b/R/epidish.R
@@ -42,8 +42,7 @@ 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_mset(methyl_set)
   beta_matrix <- minfi::getBeta(methyl_set)
 

diff --git a/R/methylResolver.R b/R/methylResolver.R
@@ -15,8 +15,6 @@
 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_mset(methyl_set) 

diff --git a/R/methylcc.R b/R/methylcc.R
@@ -29,12 +29,8 @@ run_methylcc <- function(methyl_set, array = c('450k','EPIC'),
                          init_param_method = "random", a0init = NULL, a1init = NULL,
                          sig0init = NULL, sig1init = NULL, tauinit = NULL, demo = FALSE,
                          seed = 1){
-  require(methylCC)
-  require(minfi)
-  require(FlowSorted.Blood.450k)
-  require(IlluminaHumanMethylation450kmanifest)
-
   set.seed(seed)
+  options(matrixStats.useNames.NA = "deprecated")
 
   check_input_mset(methyl_set)
 

diff --git a/R/plots.R b/R/plots.R
@@ -40,7 +40,7 @@ visualize_results <- function(result){
     df <- data.frame()
     sapply(names(result), function(m){
       df_tmp <- as.data.frame(result[[m]])
-      df_tmp <- methylDeconv:::rename_cell_types(df_tmp)
+      df_tmp <- rename_cell_types(df_tmp)
       df_tmp$other <- NULL
       df_tmp$method <- m
       df_tmp$sample <- rownames(df_tmp)
@@ -114,7 +114,7 @@ visualize_result_bar <- function(result, rename = F) {
   }
   df <- as.data.frame(result)
   if(rename){
-    df <- methylDeconv:::rename_cell_types(df)
+    df <- rename_cell_types(df)
   }
 
   df$sample <- rownames(df)
@@ -153,8 +153,8 @@ compare_results <- function(res1, res2) {
     return()
   }
 
-  df1 <- methylDeconv:::rename_cell_types(res1)
-  df2 <- methylDeconv:::rename_cell_types(res2)
+  df1 <- rename_cell_types(res1)
+  df2 <- rename_cell_types(res2)
 
   df <- merge(df1, df2, by=0, all = T)
   df$Row.names <- NULL

diff --git a/inst/deconvolve.py b/inst/deconvolve.py
@@ -1,4 +1,5 @@
-#!/nfs/home/students/l.willruth/miniconda3/envs/r-methyldeconv/bin/python -u
+## downloaded from https://github.com/nloyfer/meth_atlas
+
 import numpy as np
 import pandas as pd
 from scipy import optimize

diff --git a/tests/testthat/test_methods.R b/tests/testthat/test_methods.R
@@ -1,6 +1,6 @@
-library(methylDeconv)
-library(minfiData)
-library(minfi)
+suppressMessages(library(methylDeconv))
+suppressMessages(library(minfiData))
+suppressMessages(library(minfi))
 
 ex_data <- minfiData::MsetEx
 meth <- minfi::getMeth(ex_data)