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Questions tagged [genomicranges]

72 questions
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Aggregating scores of multiple metadata columns from one GRanges object on another

I have one GRanges object with thousands of score columns (tomap), and another with regions of interest and no metadata (roi). I am trying to map the max score from each column in tomap to the corresponding interval in roi. I also want to retain the…
polg
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Is it possible to load a Granges .Rdata file under a specific name?

I am trying to open a Granges file, and I want to store it under a specific name rather than the file name so that I can later use the file within functions and loops. The following works fine, but saves the file under the name…
Harnarday
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ISCN- from genomic coordinates

I got a large table with genomic coordinates of CNV found in our cohort: CNV chr1:146458850-148003653 I would like to add the following data to the table : International System for Human Cytogenetic Nomenclature(ISCN), cnv size, names of genes…
PSmy
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Splitting a dataframe into overlapping groups of equal sizes

I am looking for a way to split my data into groups where each group is made of the same window size I define. Chrom Start End chr1 1 10 chr1 11 20 chr1 21 30 …
user12
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How to find the nearby genes from differentially expressed locus

I am interesting in to find out the nearby gene of differentially expressed locus from bedtools. 1000 upstream and downstream genes I have a list of differentially expressed locus in .xlsx format. Now I want to know that how can I extract the gene…
Bioifo
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Add columns that sum score around range

I have a wig file that I've read into a granges-like object using a function that I wrote that calls the rtracklayer package: read_wig <- function(x, format='wig', genome='mm9') { suppressMessages(library(rtracklayer)) merged_wig <-…
user2117258
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Sampling within ranges

I have troubles to sample within a certain background or excluding some possibilities. I am trying to create a R function that shuffles genomic regions. For now the function works well and follow those steps: Retrieves all the genomic regions…
Zacharie Ménétrier
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Obtain the specific range that overlap

I have two dataframes: cnv_1 chr start end 3 62860387 63000898 12 31296219 31406907 14 39762575 39769146 19 43372386 43519442 19 56419263 56572829 cnv_2 chr start end 6 30994163 30995078 19 43403531 …
Julio Rodríguez
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How to calculate length distribution and coverage distribution bed file

I have dataset in bed file and I want to calculate and plot the length and coverage distribution of file. How can I calculate length distribution in R. df1: chr21 2800 3270 chr21 3600 4152 chr2 3719 5092 chr22 3893 4547 chr2 339 5092 chr22 3563…
user15708301
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genomic coordinate in R

I am working on the TxDb.Hsapiens.UCSC.hg19.knownGene data. I found that the length of the largest exon is 205012. How can I proceed to find the genomic coordinate of that exon?
Chris7
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How to filter for only one of many intersecting ranges

As part of a much longer and complex query, I am trying to keep only one entry for overlapping intervals, and all entries which do not overlap. Here is a minimal example: create table protein ( seqid varchar(100), start SMALLINT(5), …
fridaymeetssunday
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rolling join to find genomic regions

The Quick version is that I want to find all matches within a certain distance of certain values. Example: library(data.table) reads <- structure(list(seqnames = c(1, 1, 1, 1, 1, 1, 1), start = c(100, 100, 100, 130, 130, 132, 133), end = c(130,…
fridaymeetssunday
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