Update DiffBind_v2_EdgeR_block.Rmd

Removing up.bed and down.bed

bin/DiffBind_v2_EdgeR_block.Rmd

@@ -35,8 +35,6 @@ csvfile <- params$csvfile
 contrasts <- params$contrasts
 peakcaller <- params$peakcaller
 peak_counts <- params$counts
-down_file <- params$down_file
-up_file <- params$up_file
 list_file <- params$list_file
 ```
 
@@ -178,16 +176,6 @@ dba.plotHeatmap(DBAnalysisEdgeR, contrast=1, method=DBA_EDGER_BLOCK, correlation
 ## Top 500 or less differentially bound peaks 
 
 ```{r EdgeRReport}
-UpPeaks <- DBReportEdgeR[which(DBReportEdgeR$Fold > 0)]
-print("up ")
-print(dim(UpPeaks))
-rtracklayer::export(UpPeaks, up_file)
-
-DownPeaks <- DBReportEdgeR[which(DBReportEdgeR$Fold < 0)]
-print("down ")
-print(dim(DownPeaks))
-rtracklayer::export(DownPeaks, down_file)
-
 D2i <- length(DBReportEdgeR)
 i <- as.integer(min(c(500, as.integer(max(c(D2i, 1))))))
 DT::datatable(data.frame(DBReportEdgeR)[1:i,], rownames=F)
@@ -209,4 +197,4 @@ write.table(report2, list_file, quote=F, sep="\t", row.names=F)
 sessionInfo()
 ```
 
-<div class="tocify-extend-page" data-unique="tocify-extend-page" style="height: 0;"></div>
+<div class="tocify-extend-page" data-unique="tocify-extend-page" style="height: 0;"></div>