iterating over GRangesList
I am looping over a GRangesList but it takes ages to process. Can anyone help me optimize the code please?
groupMat <- lapply(1:length(subCvgList), function(f) {
grCluster = subCvgList[f]
lapply(1:length(regionTiles), function(x) {
idx <- findOverlaps(allRegionTilesGR[x], grCluster)
sum(grCluster$score[subjectHits(idx)])
})
}) %>% do.call(cbind, .)
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Can I directly compare the regions defined by peaks from pair-end 50 and pair-end 100 ATAC-seq?
written by Dan •
-
CNV annotation using GAIA
written by melissachua90 •
-
How to speed up averaging peak signal overlapping with domains
written by gdeniz •
-
Understanding findoverlaps function in GenomicRanges
written by alexmondaini •
-
More efficient way of lifting over and collapsing CNV GenomicRanges using rtracklayer?
written by j.torpy •
-
xml file conversion in R
written by Kira •
-
Clustering biological sequences based on numeric values
written by keshavmot2 •
-
How can i optimize distance Matrix that construct phylogenetic tree ??
written by eng_samar_zayed •
-
How to facilitate the performance of overlap for GRanges objects (verifiable example is given)?
written by Jurat Shahidin
-
Setting elementMetadata in genomicranges list objects
written by reviewer3 •
Please describe what you're doing. Add example data.