## User: foehn

foehn30
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6 days, 18 hours ago
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9 months ago
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#### Posts by foehn

<prev • 27 results • page 1 of 3 • next >
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... v1.42.2 works now. ...
written 20 days ago by foehn30
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... 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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... 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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... 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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... 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 ...
written 23 days ago by foehn30 • updated 23 days ago by Michael Lawrence10k
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... 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 ...
written 5 weeks ago by foehn30 • updated 5 weeks ago by Johannes Rainer1.4k
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... 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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... 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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... Thanks for the explanation. ...
written 6 weeks ago by foehn30
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... 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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