User: wcstcyx

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wcstcyx30
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China/Beijing/AMSS,CAS
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2 weeks ago
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Epigenomics

Posts by wcstcyx

<prev • 31 results • page 1 of 4 • next >
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Comment: C: matrix as a column of mcols of GRanges would not be extracted correctly by lappl
... Hi Michael, Thanks! I tried to understand those functions you had mentioned. And found extractROWS(gr$mat, NSBS(IRanges(1,2), gr$mat)) eventually calls x <- as(x, "vector_OR_factor", strict = FALSE) which would convert a matrix or an array to a numeric vector. And consequently the followin ...
written 3 months ago by wcstcyx30
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matrix as a column of mcols of GRanges would not be extracted correctly by lapply
... Hi, I used matrix as a column of mcols of GRanges. This kind of structure would be of great value in some case. However, I found the matrix can not be extracted correctly with lapply. I don't know the reason. I can use 'for loop' to get around of it, but this way is not very convenient.  For examp ...
granges dataframe mcols written 4 months ago by wcstcyx30 • updated 4 months ago by Michael Lawrence9.8k
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Comment: C: `precede` does not perform as expected
... The new nearest(), precede() and follow() in GenomicRanges 1.27 consider strand in a more reasonable way as you showed in the beautiful ascii table. When select = "all", the result is meaningful. > gene <- GRanges("chr1:5-6:*") > peak <- GRanges(c("chr1:1-2:+", "chr1:13-14:-", "chr1:1- ...
written 7 months ago by wcstcyx30
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Comment: C: `precede` does not perform as expected
... I can use the new precede() with selectNearest() to finish my task now. subjectHits(selectNearest(precede(erbs, ghs, select = "all"), erbs, ghs)) Thanks! By the way, selectNearest() in the IRanges package is not in the "Usage" part of its help page. Hope you can complete it. Can ...
written 7 months ago by wcstcyx30
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Comment: C: `precede` does not perform as expected
... Thanks very much for your work!!! Can ...
written 10 months ago by wcstcyx30
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Comment: C: GenomicRanges bug in follow?
... Actually, precede() and follow() gave the nearest but not overlapped range in that version. > (peak1 <- GRanges("chr1", IRanges(c(3, 7), width = 1))) GRanges object with 2 ranges and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> <Rle> [1] ...
written 10 months ago by wcstcyx30
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Comment: C: `precede` does not perform as expected
... In the end, hope orientation can be implemented to solve those problems. Thanks a lot to you and Valerie. Best regards Can ...
written 10 months ago by wcstcyx30
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Comment: C: `precede` does not perform as expected
... At last, I want to show how to solve Janet's problem and task(1)(2)(3) with old precede() and follow(). I installed Bioconductor version 3.0 (BiocInstaller 1.16.5) and GenomicRanges_1.18.4 on R 3.1.3. > (peak1 <- GRanges("chr1", IRanges(c(3, 7), width = 1))) GRanges object with 2 ranges and ...
written 10 months ago by wcstcyx30
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Comment: C: `precede` does not perform as expected
... It is a good idea to use orientation! I agree that it can sovle Janet's case, my case in this post (also task (1)), and task (2). Thanks for the long discussion. ...
written 10 months ago by wcstcyx30
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Comment: C: Any way to proceed duplicate removal for list of GRanges object ?
... Thanks. I deleted grl, but grl_expect in my answer seems more appropriate than in your post. I suggest you change foo in your grl_expected to be foo= GRanges(seqnames = Rle("chr11",11), IRanges( c(12,12,12,58,58,58,118,44,102,118,118), c(36,36,36,92 ...
written 10 months ago by wcstcyx30

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