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Questions tagged [genomicranges]

72 questions
6
votes
4 answers

Find which column ranges overlap after grouping in R

I have a huge data frame that looks like this. I want to group_by(chr), and then for each chr to find Is any range1 (start1, end1), within the chr group, overlapping with any range2 (start2,end2)? library(dplyr) df1 <- tibble(chr=c(1,1,2,2), …
LDT
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4
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1 answer

Should as.data.table method for GRanges modify the original object by reference by default?

When using the as.data.table() function from the data.table package to create a data.table out of a GRanges object, the default method is called (https://github.com/Rdatatable/data.table/blob/master/R/as.data.table.R#L8-L10). This leads to the…
Alex
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3
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1 answer

Error using makeGRangesFromDataFrame in an R workflow for ATAC-seq

New to R. Recently working through an ATAC-seq workshow in R. In Section 5.1 of where I call the makeGRangesFromDataFrame function I get the following error - > atac_esca.gr <- makeGRangesFromDataFrame(atac_esca,keep.extra.columns = T) Error in…
Ethidium Bromide
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3
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1 answer

Merging adjacent bins with same property in GenomicRanges object

Having segmented a genome into adjacent non-overlapping bins, e.g. by tileGenome, I have computed some property by some means for each bin (say either 1 or 2). Now I want to merge adjacent with the same property. An minimal example is illustrated…
Sebastian Müller
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2
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3 answers

GRanges as column in base::data.frame

I would like to store a GenomicRanges::GRanges object from Bioconductor as a single column in a base R data.frame. The reason I'd like to have it in a base R data.frame is because I'd like to write some ggplot2 functions that exclusively work with…
teunbrand
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2
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2 answers

R : Count unique element per interval

Let say I've a list of non-overlapping genomic intervals. chr1 1 100 chr1 101 200 chr1 201 300 chr1 301 400 and a list of genomic positions linked to different samples as : chr1 50 sampleA chr1 60 sampleB chr1 110…
Nicolas Rosewick
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2
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2 answers

Get ranges for synonymous and non-synonymous nucleotide positions within a codon separately

I have GRanges object (coordinates of all gene exons); coding_pos defines what is the start position of a codon in a particular exon (1 means that first nucleotide in exon is also the first nt in a codon, and so on). grTargetGene itself looks like…
lizaveta
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2
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2 answers

Granges - (left) join

I have two Granges objects and I would like them to be merge in order to combine both GRanges even if the metadata are not existing in both objects. > t GRanges object with 2 ranges and 5 metadata columns: seqnames ranges strand | …
Bratten
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2
votes
1 answer

Simulate random positions from a list of intervals

I am trying to develop a function in R to output random positions in list of given intervals. My intervals file (14,600 lines) is a tab delimited bed file (chromosome start end name) that looks like this: 1 4953 16204 1 1 16284 …
fugu
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2
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2 answers

pythonic equivalent to reduce() in R GRanges - how to collapse ranged data?

In R (albeit longwinded): Here is a test data.frame df <- data.frame( "CHR" = c(1,1,1,2,2), "START" = c(100, 200, 300, 100, 400), "STOP" = c(150,350,400,500,450) ) First I make GRanges object: gr <- GenomicRanges::GRanges( seqnames =…
mbyvcm
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2
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0 answers

setdiff with GenomicRanges: no method for coercing this S4 class to a vector

I'm using setdiff() with two GR objects and before updating R on my computer my code worked fine:…
Mariela Cortés López
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0 answers

S4Vectors::expand on granges rows based on multiple columns

I have a GRANGES object similar to below: GRanges object with 3 ranges and 2 metadata columns: seqnames ranges strand | txid txname | [1] chr1 1-3 + | 1 a [2] …
plenty_of_code
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0 answers

Generate Random Permutations of Genomic Ranges using Nullranges (matchedranges or bootranges)

I want to generate 200 random genomicranges that are 200kbp long each that can occur anywhere in the genome. I was recommended to try using nullranges, but I haven't figured out how to specify only generating 200 ranges / iteration. I think it takes…
erman
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0 answers

Concatenate consecutive iranges coordinates with same metadata value

I have this granges object: gr <- GRanges( seqnames = c(rep("chr1", 3)), IRanges(start = c(1, 10, 20), end = c(5, 15, 25)), group = c("A", "A", "B") ) I would like to concatenate the events that are the same group (f.ex A) joining the…
msevilla
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1
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2 answers

Remove hits of overlapping ranges based on another column in R

I have a large data frame that looks like this. I want to group_by seqnames and for each group, I want to check for overlapping ranges between the start and end. If there is any overlapping range, then it should stay the row with the highest…
LDT
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