User: reviewer3

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reviewer320
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6 years, 3 months ago
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Posts by reviewer3

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Comment: C: Setting elementMetadata in genomicranges list objects
... Thank you, Devon! I understand that `distanceToNearest()` respects chromosomes, but I have to do more analysis once I have the distances and I'd like to do it chromosome by chromosome as they differ in gene content, etc. Also, `end(gr2.toy) = start(gr2.toy)` isn't strand-sensitive, so the true 5' of ...
written 6.3 years ago by reviewer320 • updated 8 months ago by RamRS30k
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Setting elementMetadata in genomicranges list objects
... I thought this would be easy, but once again working with genomicranges is not intuitive to me. Here's a toy genomic ranges object. I want to generate a GR list for each chromosome, calculate the distance between the start of each feature (irrespective of strand, so in this case it's all 0, but it ...
genomicranges values elementmetadata mcols written 6.3 years ago by reviewer320 • updated 4.3 years ago by leekaiinthesky180
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Comment: C: Adding metadata to genomicranges list
... Hi Philipp, I tried both (with and without as.data.frame but get an error referring to a difference in row numbers): arguments imply differing number of rows: 589, 790, 482, 681, 698, 492, 713, 489, 590, 521, 853, 395, 373, 358, 388, 340, 465, 287, 357 ...
written 6.3 years ago by reviewer320
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Answer: A: Adding metadata to genomicranges list
... Ok, a for loop works (see below), but if some GR gurus see this, please save me from my ignorance and tell me how to do this using standard GR functions (Map , endoapply, mendoapply, Reduce). The for solution is fast enough but doesn't use the names of the objects in the lists, so it depends entirel ...
written 6.3 years ago by reviewer320
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Comment: C: Adding metadata to genomicranges list
... Hi Philipp, thanks for your answer. I tried merge but got an error. I think I have a solution using a for loop, but I'm pretty sure there's a better way to do it using Map, except that my vectors are regular numeric vectors not S4 GR objects. I'll keep hacking at it, but if you have another idea, I' ...
written 6.3 years ago by reviewer320
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Adding metadata to genomicranges list
... Dear BioStars, I have a genomic ranges (GR) list object called "lgr.test" and would like to simply add several columns to its metadata. How would I do that? I have a list of numeric vectors "lvec.test" of the same lengths as the GRs in lgr.test. Thank you! > summary(lvec.test) Length C ...
gr list genomic ranges genomicranges written 6.3 years ago by reviewer320
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Subsetting genomic ranges and plotting cirlces in ggbio used to work --- now: warnings about non-missing arguments
... I'm plotting genomic ranges in circle layout using ggbio to connect items from different categories/chromosomes via the metadata column "cross", itself an GRanges column. cp <- ggplot() + layout_circle(gr.cats, geom = "ideo", fill = "white", radius = 30, trackWidth = 4) cp.link<- cp + layou ...
ggbio ggplot2 genomic ranges written 6.4 years ago by reviewer320 • updated 5.3 years ago by Biostar ♦♦ 20
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Comment: C: genomicranges outside sequence bounds
... And, which(end(mygr) > seqlengths(BSgenome.Hsapiens.UCSC.hg19)[as.character(seqnames(mygr))]) gives me the same exact answer. Thank you! ...
written 6.4 years ago by reviewer320 • updated 9 months ago by RamRS30k
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Comment: C: genomicranges outside sequence bounds
... Thank you, seidel @seidel which(mygr.original != mygr.trimmed) gave me exactly what I needed. I got the sense that these gr containers aren't very intuitive to use, but this is obviously a great example where they are. Thank you! ...
written 6.4 years ago by reviewer320 • updated 9 months ago by RamRS30k
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genomicranges outside sequence bounds
... Hi, I'm new to genomic ranges and getting a bit frustrated with it. I'm reading the reference manual and tutorials, but haven't found an answer to the following question: I've constructed my gr object and assigned sequence lengths to it. I must have made an error, as I'm getting the warning: In v ...
genomic ranges genomicranges gr written 6.4 years ago by reviewer320 • updated 6.4 years ago by seidel7.1k

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Scholar 6.3 years ago, created an answer that has been accepted. For A: Adding metadata to genomicranges list

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