Merge pull request #33 from vyepez88/code_cleaning

overview updated
gagneurlab · Apr 15, 2020 · 9ae6722 · 9ae6722
2 parents dc80c90 + 8e0f178
commit 9ae6722
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Showing 3 changed files with 5 additions and 9 deletions.
diff --git a/drop/template/Scripts/AberrantExpressionAnalysis/Overview.R b/drop/template/Scripts/AberrantExpressionAnalysis/Overview.R
@@ -90,6 +90,7 @@ outrider_links <- sapply(annotations, get_html_path,
 #' 
 
 #' ## Analyze Individual Results
+# Read the first ods object and results table
 ods <- readRDS(snakemake@params$odsFiles[[1]])
 res <- fread(snakemake@params$resultTables[[1]])
 

diff --git a/drop/template/Scripts/AberrantSplicingAnalysis/Overview.R b/drop/template/Scripts/AberrantSplicingAnalysis/Overview.R
@@ -78,9 +78,7 @@ fraser_links <- get_html_path(datasets = datasets,
 
 #'
 #' ## Analyze individual results
-#' 
-
-# Load the files
+# Read the first fds object and results table
 fds <- loadFraseRDataSet(file = snakemake@params$fds_files[[1]])
 res <- fread(snakemake@params$result_tables[[1]])
 

diff --git a/drop/template/Scripts/MAEAnalysis/Overview.R b/drop/template/Scripts/MAEAnalysis/Overview.R
@@ -50,13 +50,10 @@ suppressPackageStartupMessages({
 #' 
 
 #' ## Analyze Individual Results
-#' 
-file <- snakemake@params$results_tables[[1]]
-res <- fread(file)
-
-file_location <- strsplit(file, "/")[[1]]
+# Read the first results table
 res_sample <- readRDS(snakemake@params$results_obj[[1]])
 
+#+echo=F
 if(is.null(res_sample$rare)){
   g1 <- plotMA4MAE(res_sample)
   g2 <- plotAllelicCounts(res_sample)
@@ -75,6 +72,6 @@ g2
 #' 
 #' [QC Overview](`r "./Scripts_QC_Datasets.html"`)
 #' 
-#' DNA-RNA matrix: 
+#' ### DNA-RNA matrix: 
 #' `r paste('* ', snakemake@params$qc_matrix, collapse='\n')`