Questions tagged [genomicranges]
The genomicranges tag has no usage guidance.
13
questions
2
votes
1
answer
40
views
Assign score to PyRanges from another PyRanges object
I have two PyRanges objects. PR1 is a set of regions of interest across a chromosome, PR2 tiles the genome and has a score associated with each range.
I need a way to get for each range in PR1 its ...
- 300
3
votes
1
answer
98
views
Find a genomic coordinates for a protein aminoacid position
Is there a function that can map genomic position (hg19) back from a protein position? I can have name of a particular transcript, and exon number.
For example, I have KRAS gene for which I would like ...
- 203
3
votes
2
answers
831
views
How to subset a GRanges object based on a specific genomic window of interest?
Goal: To keep only rows of a GRanges object if their start coordinate is within 1 Mb of the start coordinate of a gene of interest.
I am aware of some functions that come close:
...
- 115
1
vote
2
answers
178
views
Pulling a numbered chromosome range file given a gene location from a lookup table ideally from command line or R
have a folder with roughly 1000 vcf files which have divided the human genome into chunks, the folder looks like this:
...
- 153
1
vote
1
answer
181
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 ...
- 595
-1
votes
2
answers
71
views
Calculating the number of probes for a given genomic range
I have a big data frame like this for copy number (exome seq)
...
- 1,791
2
votes
0
answers
31
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 ...
- 192
0
votes
2
answers
221
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:
...
- 105
4
votes
1
answer
182
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 ...
- 496
2
votes
3
answers
199
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:
...
- 353
4
votes
1
answer
198
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:
...
1
vote
1
answer
667
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 ...
- 367
6
votes
3
answers
1k
views
How to subset a GRanges via an argument passed into a function?
Let's say I have following example GRanges:
...
- 1,373