Questions tagged [iranges]

IRanges is a Bioconductor package: Infrastructure for manipulating intervals on sequences

The package provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially (formally defined as Vector objects), as well as views on these Vector objects. Efficient list-like classes are also provided for storing big collections of instances of the basic classes. All classes in the package use consistent naming and share the same rich and consistent "Vector API" as much as possible.

Author: H. Pagès, P. Aboyoun and M. Lawrence Maintainer: Bioconductor Package Maintainer

Citation (from within R, enter citation("IRanges")):

Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, Gentleman R, Morgan M and Carey V (2013). “Software for Computing and Annotating Genomic Ranges.” PLoS Computational Biology, 9.

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Fast way to find overlaps in linear intervals

I have a data.frame of linear intervals (genomic coordinates of mapped RNA-seq reads), for example: df <- data.frame(seqnames = c(rep("chr10",2),rep("chr5",8)), start =…
dan
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Finding overlap in dataframe ranges in R

I have two bedfiles as dataframes in R, for which I want to map all overlapping regions to each other (similar to what bedtools closest would be able to do). BedA: chr start end 2 100 500 2 200 250 3 275 …
kEks
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Combining IRanges objects and maintaining mcols

I'll start with an example, and then describe the logic I'm trying to use. I have two normal IRanges objects that span the same total range, but may do so in a different number of ranges. Each IRanges has one mcol, but that mcol is different across…
rcorty
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Splitting overlapping rows, within groups, based on dates

I'm trying to create new rows based on overlapping time periods of existing rows. For example, I'd like to turn this: Customer_Product <- data.table(Customer=c("A01","A01","A01", "A02", "A02", "A02", "A03", "A03", "A03"), …
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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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Function coverage () in R

I want to understand what the function coverage does to an IRange. for example the codes below: ir <- IRanges (1:3, width = 3) ir IRanges object with 3 ranges and 0 metadata columns: start end width …
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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 …
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Integer overflow with package `IRanges` in `R`

Problem I am using the package [IRanges][1] and am in need to accurately code for very long sequences that overpass 2^31 by about 10-fold. From the following, it seems that IRanges uses int32 ##### INSTALLATION FROM SRC CODE ###### ## try http:// if…
Remi.b
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check in which range a number falls and return a new column with corresponding shift

I have two data frames ch and shift. In data frame ch i have a column with name pos which contains numbers as shown below. In data frame shift i have three columns with name shft, start and end. ch <- structure(list(pos = c(3.25, 3.75, 4.25, 4.75,…
Chanti
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How to use GenomicRanges to find overlaps by percentage of interval coverage

I have two dataframes one with two (or more) individuals (denoted by sampleID) denoted by TEST and the other consisting of just 3 columns called REF. I want to add REF onto TEST based upon the overlaps between the "chr","start","end" columns of REF…
Kaleb
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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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using r to check the shift in manufacturing plant based on the timestamp

By using the timestamp of produced unit, i want to check in which shift it was produced. Basically the production is carried out in two shifts per day. shifts timings are 06:00 to 18:00 and 18:00 to 06:00. shifts data frame below shows the planning…
Chanti
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