Questions tagged [genomicranges]

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1answer
37 views

Retrieve overlap widths with Bioconductor

I want to retrieve all overlaps between two sets of genomic intervals (GRanges) using Bioconductor. I am interested in the widths of the resulting overlapping ranges. In cases with discontinuous ...
-2
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2answers
70 views

Calculating the number of probes for a given genomic range

I have a big data frame like this for copy number (exome seq) ...
3
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0answers
27 views

What Cellbase resources are 0-indexed, and which are 1-indexed?

The UCSC Genome Browser Team is clear about that the genome browser GUI indexing which is 1-based, closed interval. Genomic sequence retrieval via the UCSC REST API is 1-based, closed interval. All ...
1
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2answers
125 views

GenomicRanges: get nearest neighbor distances for random genes using a for loop

I want to compute the nearest neighbour distances using a for loop. I can do this with a random subset by doing this: ...
5
votes
1answer
121 views

Find intervals that genes fall within their range

I am trying to run some frequency based stats to identify selective sweep in my study system using Rpackage "PopGenome". To proceed with it I have split my genome data (whole genome sequencing) into ...
2
votes
3answers
125 views

Getting a stretch of genomic ranges from a dataframe/granges object based on metadata column

I have a "test" data.frame object in R, which is basically a small subset of a 66000 row dataframe, which looks as follows: ...
4
votes
1answer
114 views

How to find genomic overlaps faster?

I was trying to find a way to find overlaps between two genomic ranges. I found a post at Biostars but it couldn't consider the chromosome information. For example: ...
2
votes
1answer
421 views

Expand granges object different amounts upstream vs. downstream

I am attempting to get gene regions and their immediate neighborhoods using Bioconductor GenomicRanges packages. It is very easy for me to extend the regions around genes if I want to extend it the ...
6
votes
3answers
673 views

How to subset a GRanges via an argument passed into a function?

Let's say I have following example GRanges: ...