Removed all extra files created during build

R/EGRET.R

@@ -56,6 +56,9 @@
 #' \donttest{
 #' runEgret(qtl,vcf,qbic,motif,expr,ppi,nameGeneMap,tag)
 #' }
+#' file.remove("my_toy_egret_run_egret.RData")
+#' file.remove("my_toy_egret_run_panda.RData")
+#' file.remove("priors_my_toy_egret_run.txt")
 #' @export
 
 runEgret <- function(b,v,q,m,e,p,g,t){

R/LIONESS.R

@@ -41,6 +41,7 @@
 #'     motif_file = motif_file_path, ppi_file = ppi_file_path, 
 #'     modeProcess="union",start_sample=1, end_sample=1, precision="single")
 #' }
+#' unlink("lioness_output", recursive=TRUE)
 #' @import reticulate
 #' @export
 lionessPy <- function(expr_file, motif_file=NULL, ppi_file=NULL, computing="cpu", precision="double", save_tmp=TRUE, modeProcess="union", remove_missing=FALSE, start_sample=1, end_sample="None", save_single_network=FALSE, save_dir="lioness_output", save_fmt='npy'){

R/pandaToAlpaca.R

@@ -34,6 +34,14 @@
 #'  
 #' # Run ALPACA
 #' alpaca<- pandaToAlpaca(treated_panda_net, control_panda_net, "./TB", verbose=TRUE)
+#' 
+#' # Delete files.
+#' file.remove("TB_ALPACA_ctrl_memb.txt")
+#' file.remove("TB_ALPACA_final_memb.txt")
+#' file.remove("TB_ALPACA_scores.txt")
+#' file.remove("TB_DWBM.txt")
+#' file.remove("TB_DWBM_colnames.txt")
+#' file.remove("TB_DWBM_rownames.txt")
 #' }
 #' 
 #' @export

tests/testthat/test-lioness.R

@@ -5,6 +5,7 @@ test_that("lionessPy() function works", {
 
   # test 1: check test error message when empty inputs
   expect_error(lionessPy())
+  unlink("lioness_output", recursive=TRUE)
 
   # input file path
   system("curl -O  https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/expr4_200_L.txt")
@@ -79,7 +80,6 @@ test_that("lioness() function works for network.inference.method = 'pearson'", {
   expect_equal(lionessNets[[2]],ssNet2,tolerance=1e-15) 
   expect_equal(lionessNets[[3]],ssNet3,tolerance=1e-15) 
   expect_equal(lionessNets[[4]],ssNet4,tolerance=1e-15) 
-
 })
 
 test_that("lioness() function throws appropriate error for undefined network.inference.method", {
@@ -91,6 +91,5 @@ test_that("lioness() function throws appropriate error for undefined network.inf
 
   # run LIONESS on the toy data w/undefined method
   expect_error(lioness(expr=t(X),network.inference.method="divination"))
-
 })
 

vignettes/ApplicationinGTExData.Rmd

@@ -195,6 +195,9 @@ The result is a data frame in which the first colum  contains TFs, the second co
 lionessLCL[1:5,1:10]
 ```
 
-
+## Remove output directory.
+```{r}
+unlink("lioness_output", recursive=TRUE)
+```
 
 

vignettes/LionessApplicationinGTExData.Rmd

@@ -182,4 +182,4 @@ g+geom_point(aes(fill=NES), shape=21, colour="white")+
   scale_fill_gradient2(low=dencol_neg, high=dencol_pos)+
   theme(axis.text.y = element_text(colour=signcol))+
   theme(aspect.ratio=asp, axis.title.y=element_blank()) # test aspect.ratio
-```
+```