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Questions tagged [genomicranges]

72 questions
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Can convert Granges to data.frame

I have follow data: # you can input data by run following script in Rstudio R_gui or R # this is a dput output # so you can run it for import data library(GenomicRanges) gr_test <- new("GRanges", seqnames = new("Rle", values = structure(1L, …
zhang
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Combine GRangesList with unified breakpoints

I'm looking to merge a list of 6 GRanges objects into one, with the resulting table have a common set of breakpoints across all 6 objects as shown in Figure 1 below. I've tried to do this using findOverlaps(), however the this is equivalent to a…
RodrigoGM
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How to get findOverlapped region?

Hi i am working with GRanges and finding the overlaps using findOverlaps function of IRanges. I am getting the hits of which query and subject are overlapped,but I want to also have the coordinates of query and subject where they are overlapped…
user15708301
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R: For loop to subset Granges objects by list

I have a txf_df which I subset by gene.list$entrez and then found the list of unique number of transcripts. The txf_df is then converted to txf_grange. Now, I want to create a for loop of the 15 unique genes, where upon each iteration, subset the…
melolili
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How to remove overlapping sequences from two datatables?

I have two data.tables that provide sequence coordinates across different chromosomes (categories). For example: library(data.table) dt1 <- data.table(chromosome = c("1", "1", "1", "1", "X"), start = c(1, 50, 110, 150, 110), …
Powege
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Overlapping and sorting counts from small, equally sized, continuous bins into irregular, uneven bins

I really appreciate if you are reading this and taking your precious time to help me with a problem I have. In R, I would like to sort data from small, continuous bins from one dataframe to the (non-overlapping) bins of irregular size and…
LawrenceThundersthorp
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Finding overlaps between 2 ranges and their overlapped region lengths?

I need to find length of overlapped region on same chromosomes between 2 group(gp1 & gp2). (similar question in stackoverflow were different from my aim, because I wanna find overlapped region not a TRUE/FALSE answer). For example: gp1: chr start…
hiam
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Error in as.vector(x) : no method for coercing this S4 class to a vector

I am trying to run an R script on the command line of bash (I am using CentOS 8) with the command: cat 1_myScript.R | R --slave --args $SAMPLE"_x" $SAMPLE"_y" where $SAMPLE is an argument that I have specified in the R script as follows >…
Giuseppe D'alterio
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A fast way tp spread a linear range

I have a data.frame where each row is a linear interval - specifically these intervals are start and end coordinates on chromosomes (chr below): df <- data.frame(chr = c("chr1","chr2","chr2","chr3"), strand = c("+","+","-","-"), …
dan
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Compare two genomic ranges (R)

I have 2 genomic ranges g1<-GRanges(c("chr1:0-14","chr1:15-29"), score=c(20.2,10.4));g1 GRanges object with 2 ranges and 1 metadata column: seqnames ranges strand | score | [1] chr1 0-14 …
i love mistaking
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Genomic Ranges - Merge Overlaps in Single File (R STUDIO)

I would like to find overlapped regions in the file and merge them keeping the earlier start and the later stop (merge 2 regions in 1) I meant to use Genomic Ranges but I am not sure how to code the script. This is what the file fileA.txt…
Kaitsja
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Adapt metadata of a GenomicRanges object when disjoined

I have a GRanges object with some genomic intervals and some metadata (3 vectors with the coverage of each region in 3 different samples). I have applied: disjoin(my_data) to obtain a new GRanges object with the smallest set of unique,…
Jeni
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Problem with CoverageHeatmap (Bioconductor) function in R

I have 2 sets of pairwise alignments, where query genome 1 (q1) is aligned to the reference genome and query genome 2 (q2) is aligned to the same reference genome. Therefore, I have both alignments with a coordinate system in the reference genome.…
Charlie W
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Error with the GenomicFeatures function "transcriptsByOverlaps()" in R

Retrieved the DNA sequence from chromosome1, thanks to the subseq() function and the DNAString function (from biomaRt), my goal is to find all the possible transcripts into this sequence. I thought to find the overlaps between the GRange object…
LenMar
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Find Islands in GenomicRanges

In GenomicRanges one interesting problem is the identification of gene islands. I am trying to find the largest subset of ranges in which neighboring ranges dont exceed a certain distance. To solve the issue I have tried to assign groups based on…
Peter Pisher
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