User: lee.s

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lee.s40
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Posts by lee.s

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Comment: C: extracting gene names, gene id and transcript id
... Yes you're right, thanks! - the backend of the readers use import so read_gff() should still work. I should update plyranges to explicitly include gtf. ...
written 10 months ago by lee.s40
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Comment: C: the closest gene to a breakpoint
... Another option is to use join_nearest() or pair_nearest() from plyranges ...
written 10 months ago by lee.s40
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Answer: A: extracting gene names, gene id and transcript id
... Another option with plyranges library(plyranges) gr <- read_gff("your_file.gtf") %>% select(gene_id, gene_name, transcript_id) ...
written 10 months ago by lee.s40
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Comment: C: subsetByOverlaps : comparing GRANGES and keeping all the information in the MET
... Hi Bogdan, You need R >= 3.5 so you can use Bioc 3.7. Thanks, Stuart ...
written 10 months ago by lee.s40
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Answer: A: subsetByOverlaps : comparing GRANGES and keeping all the information in the MET
... Hi Bogdan, Using plyranges join functions should get you what you want, with the caveat that identifiers need to be columns of a GRanges rather than rownames library(plyranges) ## DNAse gr2 <- GRanges("chr1", IRanges(8:12, width=5), score2=10:14, id=paste0("dnase:", letters[1:5])) ## SNP gr1 < ...
written 10 months ago by lee.s40
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Comment: C: Compute average score across multiple bed files
... In their example it looks like they want a count since all their scores are equal to three ...
written 11 months ago by lee.s40
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Answer: A: Compute average score across multiple bed files
... Updated to reflect Michael's comments: Here's a way with plyranges and one with GenomicRanges. suppressPackageStartupMessages(library(plyranges)) a <- GRanges("chr1:10-20", score = 3) b <- GRanges("chr1:12-14", score = 3) c <- GRanges("chr1:16-18", score = 3) bind_ranges(a,b,c) %>% ...
written 11 months ago by lee.s40

Latest awards to lee.s

Scholar 11 months ago, created an answer that has been accepted. For A: subsetByOverlaps : comparing GRANGES and keeping all the information in the MET
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: subsetByOverlaps : comparing GRANGES and keeping all the information in the MET

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