Merge pull request #139 from stemangiola/improve-diff-tissue-composition

Improve diff tissue composition
stemangiola · Jan 12, 2021 · 96844b0 · 96844b0
2 parents 605bb4a + 67d70f0
commit 96844b0
Show file tree

Hide file tree

Showing 13 changed files with 403 additions and 162 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -64,7 +64,8 @@ Suggests:
     pasilla,
     ggrepel,
     devtools,
-    functional
+    functional,
+    immunedeconv
 VignetteBuilder: 
     knitr
 RdMacros:

diff --git a/NAMESPACE b/NAMESPACE
@@ -110,6 +110,7 @@ importFrom(purrr,map)
 importFrom(purrr,map2)
 importFrom(purrr,map2_dfr)
 importFrom(purrr,map_dfr)
+importFrom(purrr,map_lgl)
 importFrom(purrr,reduce)
 importFrom(purrr,when)
 importFrom(rlang,":=")
@@ -143,7 +144,10 @@ importFrom(stats,rnorm)
 importFrom(stats,sd)
 importFrom(stats,setNames)
 importFrom(stats,terms)
+importFrom(stringr,str_remove)
 importFrom(stringr,str_replace)
+importFrom(stringr,str_replace_all)
+importFrom(stringr,str_split)
 importFrom(tibble,as_tibble)
 importFrom(tibble,tibble)
 importFrom(tidyr,complete)

diff --git a/R/cibersort.R b/R/cibersort.R
@@ -64,8 +64,9 @@ CoreAlg <- function(X, y, cores = 3){
   }
 
   #Execute In a parallel way the SVM
-  if(Sys.info()['sysname'] == 'Windows') out <- mclapply(1:svn_itor, res, mc.cores=1) else
-    out <-  mclapply(1:svn_itor, res, mc.cores=cores) #lapply(1:svn_itor, res) #
+  if(Sys.info()['sysname'] == 'Windows') out <- mclapply(1:svn_itor, res, mc.cores=1) 
+  else if(cores>1) out <-  mclapply(1:svn_itor, res, mc.cores=cores) 
+  else out <-  lapply(1:svn_itor, res)
 
   #Initiate two variables with 0
   nusvm <- rep(0,svn_itor)