Add get_actual_path

neurogenomics · Jan 24, 2022 · bc23b54 · bc23b54
1 parent 3ed7507
commit bc23b54
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Showing 2 changed files with 3 additions and 0 deletions.
diff --git a/R/magma_read_covar_out.R b/R/magma_read_covar_out.R
@@ -7,6 +7,7 @@
 #' @keywords internal 
 magma_read_covar_out <- function(out_prefix){
     path <- sprintf("%s.gsa.out", out_prefix)
+    path <- get_actual_path(path)
     res <- read.table(file = fix_path(path), 
                       header = TRUE,
                       stringsAsFactors = FALSE)  

diff --git a/R/magma_read_sets_out.R b/R/magma_read_sets_out.R
@@ -9,6 +9,7 @@
 magma_read_sets_out <- function(out_prefix,
                                 verbose = TRUE){  
     sets.out <- sprintf("%s.sets.out",out_prefix)
+    sets.out <- get_actual_path(sets.out)
     if(file.exists(sets.out)){
         messager("Reading sets out info from .set.out file.",
                  v=verbose) 
@@ -20,6 +21,7 @@ magma_read_sets_out <- function(out_prefix,
                  v=verbose)
         #### Not totally sure if this is right
         path <- sprintf("%s.gsa.out", out_prefix)
+        path <- get_actual_path(path)
         res <- utils::read.table(file = fix_path(path),
                                   header = TRUE,
                                   stringsAsFactors = FALSE)