Recursive dir.create

brucemoran · Nov 24, 2020 · a710e60 · a710e60
1 parent fc838bd
commit a710e60
Show file tree

Hide file tree

Showing 9 changed files with 14 additions and 14 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -10,7 +10,7 @@ export(found_in_three)
 export(found_in_two)
 export(genesGTF)
 export(get_metadata)
-export(get_tx2gen)
+export(get_tx2gene)
 export(limma_module)
 export(master_parse_join)
 export(nf_core_rnaseq_featco_parser)

diff --git a/R/DESeq2_module.R b/R/DESeq2_module.R
@@ -47,7 +47,7 @@ DESeq2_module <- function(count_data, anno_tb = NULL, tpm_tb = NULL, tag = NULL,
     output_dir <- "./DEseq2"
   } else {
     output_dir <- paste0(output_dir, "/DEseq2")
-    dir.create(output_dir, showWarnings = FALSE)
+    dir.create(output_dir, recursive = TRUE, showWarnings = FALSE)
   }
 
   ##read in condition data

diff --git a/R/edgeR_module.R b/R/edgeR_module.R
@@ -42,7 +42,7 @@ edgeR_module <- function(count_data, anno_tb = NULL, tpm_tb = NULL, tag = NULL,
     output_dir <- "./edgeR"
   } else {
     output_dir <- paste0(output_dir, "/edgeR")
-    dir.create(output_dir, showWarnings = FALSE)
+    dir.create(output_dir, recursive = TRUE, showWarnings = FALSE)
   }
 
   ##read in condition data

diff --git a/R/fgsea.R b/R/fgsea.R
@@ -97,7 +97,7 @@ fgsea_plot <- function(res, sig_res = NULL, msigdb_species = "Homo sapiens", msi
 
   ##plotting
   out_dir <- paste0(output_dir, "/fgsea")
-  dir.create(out_dir, showWarnings = FALSE)
+  dir.create(out_dir, recursive = TRUE, showWarnings = FALSE)
   gg_fgsea <- ggplot2::ggplot(fgsea_res_sig_tb, ggplot2::aes(reorder(pathway, NES), NES)) +
               ggplot2::geom_col(ggplot2::aes(fill = padj)) +
               ggplot2::coord_flip() +

diff --git a/R/limma_module.R b/R/limma_module.R
@@ -40,7 +40,7 @@ limma_module <- function(count_data, anno_tb = NULL, tpm_tb = NULL, tag = NULL,
     output_dir <- "./limma"
   } else {
     output_dir <- paste0(output_dir, "/limma")
-    dir.create(output_dir, showWarnings = FALSE)
+    dir.create(output_dir, recursive = TRUE, showWarnings = FALSE)
   }
 
   ##read in condition data

diff --git a/R/post_module_joins.R b/R/post_module_joins.R
@@ -168,7 +168,7 @@ venn_3 <- function(master_list, tag, output_dir, padj = 0.01){
     ##compare those lists
     vdf <- cbind(unc, unlist(lapply(compf_list, length)))
     colnames(vdf) <- c(names(master_list), "Counts")
-    dir.create(paste0(output_dir, "/venn_3"), showWarnings = FALSE)
+    dir.create(paste0(output_dir, "/venn_3"), recursive = TRUE, showWarnings = FALSE)
     readr::write_csv(as.data.frame(vdf), path = paste0(output_dir, "/venn_3/", tag, ".", contrast, ".venn_3.csv"))
 
     ##write venn

diff --git a/R/prep_RNAseq_output.R b/R/prep_RNAseq_output.R
@@ -69,7 +69,7 @@ brucemoran_rnaseq_kallisto_parser <- function(metadata_csv, data_dir = NULL, agg
 
   ##annotation to use
   print("Getting tx2gene object")
-  tx2gene <- get_tx2gen(genome_prefix)
+  tx2gene <- RNAseqR::get_tx2gene(genome_prefix)
 
   if(genome_prefix != "hsapiens"){
     tx2gene1 <- tx2gene
@@ -99,7 +99,7 @@ brucemoran_rnaseq_kallisto_parser <- function(metadata_csv, data_dir = NULL, agg
 #' @return tx2gene format for sleuth_prep() in get_abundance_tsv()
 #' @export
 
-get_tx2gen <- function(genome_prefix){
+get_tx2gene <- function(genome_prefix){
 
   datasets <- biomaRt::listDatasets(biomaRt::useMart("ensembl"))
   datasetm <- paste0(genome_prefix, "_gene_ensembl")

diff --git a/R/wrapper_scripts.R b/R/wrapper_scripts.R
@@ -26,7 +26,7 @@ run_prep_modules_bm <- function(metadata_csv, metadata_design, tag, output_dir =
   ##create an output called RNAseqR in current dir if no output_dir defined
   if(is.null(output_dir)){
     output_dir <- paste0(getwd(), "/", tag, "/RNAseqR")
-    dir.create(output_dir, showWarnings = FALSE)
+    dir.create(output_dir, recursive = TRUE, showWarnings = FALSE)
   }
 
   ##prepare data and save
@@ -39,7 +39,7 @@ run_prep_modules_bm <- function(metadata_csv, metadata_design, tag, output_dir =
   tpm_tb <- tpm_tb <- sot[[1]]$obs_raw_tpm$wide
   anno_tb <- tibble::as_tibble(sot[[2]])
   outdir <- paste0(output_dir, "/inputs")
-  dir.create(outdir, showWarnings = FALSE)
+  dir.create(outdir, recursive = TRUE, showWarnings = FALSE)
   save(count_data, tpm_tb, anno_tb, file = paste0(outdir, "/", tag, ".count_tpm_anno.RData"))
 
   ##run modules
@@ -95,5 +95,5 @@ run_prep_modules_bm <- function(metadata_csv, metadata_design, tag, output_dir =
   })
 
   save(master_list, fitwo_list, fithree, fgsea_list,
-       paste0(outdir, "/", tag, ".full_results.RData")
+       paste0(outdir, "/", tag, ".full_results.RData"))
 }
diff --git a/man/get_tx2gen.Rd → man/get_tx2gene.Rd b/man/get_tx2gen.Rd → man/get_tx2gene.Rd