Speed improvements

Huising-Lab · Nov 18, 2023 · cfd86fd · cfd86fd
1 parent b415de5
commit cfd86fd
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Showing 3 changed files with 4 additions and 3 deletions.
diff --git a/R/epiRomics_chromatin_tracks.R b/R/epiRomics_chromatin_tracks.R
@@ -9,7 +9,6 @@ epiRomics_chromatin_tracks <-
   function(epiRomics_gene_name,
            epiRomics_dB,
            epiRomics_track_connection) {
-    Gviz::GeneRegionTrack(eval(parse(text = epiRomics_dB@txdb)))
     epiRomics_entrez_id <-
       base::as.vector(AnnotationDbi::mapIds(
         base::eval(base::parse(text = epiRomics_dB@organism)),
@@ -21,6 +20,7 @@ epiRomics_chromatin_tracks <-
       GenomicFeatures::genes((base::eval(base::parse(text = epiRomics_dB@txdb))))
     epiRomics_gene_map_track <-
       epiRomics_gene_map[epiRomics_gene_map$gene_id == epiRomics_entrez_id, ]
+    #Gviz::GeneRegionTrack(eval(parse(text = epiRomics_dB@txdb)), start = epiRomics_gene_map_track@ranges@start, end = data.frame(epiRomics_gene_map_track@ranges)$end, chromosome = epiRomics_gene_map_track@seqnames@values)
     # Uncommented the below line to fix max width issue for certain genes, such as MafA
     epiRomics_gene_map_track <-
       GenomicRanges::resize(
@@ -46,6 +46,7 @@ epiRomics_chromatin_tracks <-
     itrack <- Gviz::IdeogramTrack(genome = "mm10", chromosome = chr)
     epiRomics_track_connection_chromatin <-
       epiRomics_track_connection[epiRomics_track_connection$type == "atac", ]
+
     range_max <-
       maxCovFiles(
         epiRomics_track_connection_chromatin[, 1],

diff --git a/R/epiRomics_track_layer.R b/R/epiRomics_track_layer.R
@@ -10,7 +10,7 @@
 epiRomics_track_layer <- function(epiRomics_putative_enhanceosome, epiRomics_index, epiRomics_dB, epiRomics_track_connection, epiRomics_keep_epitracks = TRUE) {
   epiRomics_class_save <- epiRomics_putative_enhanceosome
   epiRomics_putative_enhanceosome <- epiRomics_putative_enhanceosome@annotations[epiRomics_index, ]
-  Gviz::GeneRegionTrack(eval(parse(text = epiRomics_class_save@txdb)))
+  #Gviz::GeneRegionTrack(eval(parse(text = epiRomics_class_save@txdb)))
   chr <- base::as.character(BiocGenerics::unique(GenomeInfoDb::seqnames(epiRomics_putative_enhanceosome)))
   gtrack <- Gviz::GenomeAxisTrack()
   txTr <- Gviz::GeneRegionTrack(base::eval(base::parse(text = epiRomics_class_save@txdb)),

diff --git a/R/utils.R b/R/utils.R
@@ -10,7 +10,7 @@
 #'
 #' @noRd
 maxCovBw <- function(bw, gr) {
-  ovlp <- IRanges::subsetByOverlaps(rtracklayer::import(bw), gr)
+  ovlp <- IRanges::subsetByOverlaps(rtracklayer::import(bw, format="BigWig", selection=BigWigSelection(gr)), gr)
   if (length(ovlp) > 0) {
     print("not empty")
     max_cov <- max(ovlp$score)