User: foehn

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foehn30
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Posts by foehn

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Comment: C: How to set track attributes in rtracklayer
... v1.42.2 works now. ...
written 20 days ago by foehn30
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Comment: C: How to set track attributes in rtracklayer
... Very clear, thanks! Also, it seems bit tricky of bioconductor's versioning, as I would think 1.43.2 should naturally contain the bug fix from 1.42.2... ...
written 23 days ago by foehn30
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Comment: C: How to set track attributes in rtracklayer
... This is the result from the latest version. It appears something is still wrong.... Any idea? Thanks again. ```r > gr1 <- GRanges("chr1", IRanges(100001, 102000)) > gr2 <- gr1 + 3000 > session <- browserSession("UCSC") > track(session, name = "gr1", color = col2rgb("red")[, 1], ...
written 23 days ago by foehn30
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Comment: C: How to set track attributes in rtracklayer
... Indeed, my current rtracklayer is version 1.42.1. I will try 1.42.2, thanks. ...
written 23 days ago by foehn30
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How to set track attributes in rtracklayer
... Hello, I'm trying to use rtracklayer to view my data in UCSC genome browser, but have no idea how to set track attributes such as color or description. Manually setting up color and description in UCSC browser is rather tedious, so I would best avoid it but do it in the program. Here is an examp ...
rtracklayer browserview browsersession written 23 days ago by foehn30 • updated 23 days ago by Michael Lawrence10k
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How to use EnsDb in annotatePeak from package "ChIPseeker"
... Hello, I'm trying to use `EnsDb.Hsapiens.v86` as the annotation database for function `annotatePeak` from package "ChIPseeker". Yet I met a problem that the argument `TxDb` doesn't accept an `EnsDb` object: ``` library(EnsDb.Hsapiens.v86) library(ChIPseeker) EnsHg38 <- EnsDb.Hsapiens.v86 seqlev ...
chipseeker granges txdb annotatepeak ensdb written 5 weeks ago by foehn30 • updated 5 weeks ago by Johannes Rainer1.4k
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Comment: C: mclapply to loop over a GRangesList object
... I understand what you mean, and I agree there should be no fundamental difference. As mentioned before, the first step of `mclapply` is to convert `GRangesList` to `list`, which is time consuming and runs with only one core. Using an external index will avoid this step but distribute the cost to mul ...
written 6 weeks ago by foehn30
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Answer: A: mclapply to loop over a GRangesList object
... With regard to the original goal, one workaround is to create an external list to index the `GRangesList`: ```r index <- seq_along(GRsList) res <- mclapply(index, FUN = function(i) gaps(GRsList[[i]]), mc.cores = 4) ``` Here `gaps` can be any other procedures applied to a `GRanges` object. ...
written 6 weeks ago by foehn30
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Comment: C: mclapply to loop over a GRangesList object
... Thanks for the explanation. ...
written 6 weeks ago by foehn30
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Answer: A: mclapply to loop over a GRangesList object
... so, if the goal is to get introns per transcript, thanks to @martin's suggestion, we can use the method under the hood of `intronsByTranscript`: ```r exonsByTx <- exonsBy(EnsDb.Hsapiens.v86, "tx") tx <- transcripts(EnsDb.Hsapiens.v86) tx <- tx[match(names(exonsByTx), mcols(tx)[, "tx_id"])] ...
written 6 weeks ago by foehn30 • updated 6 weeks ago by Martin Morgan ♦♦ 23k

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