User: wcstcyx

gravatar for wcstcyx
wcstcyx30
Reputation:
30
Status:
New User
Location:
China/Beijing/AMSS,CAS
Last seen:
8 hours ago
Joined:
9 months, 2 weeks ago
Email:
w******@gmail.com

Epigenomics

Posts by wcstcyx

<prev • 30 results • page 1 of 3 • next >
0
votes
1
answer
35
views
1
answer
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 days ago by wcstcyx30 • updated 4 days ago by Michael Lawrence9.3k
0
votes
1
answers
337
views
1
answers
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 3 months ago by wcstcyx30
0
votes
1
answers
337
views
1
answers
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 3 months ago by wcstcyx30
0
votes
1
answers
337
views
1
answers
Comment: C: `precede` does not perform as expected
... Thanks very much for your work!!! Can ...
written 6 months ago by wcstcyx30
0
votes
2
answers
675
views
2
answers
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 6 months ago by wcstcyx30
0
votes
1
answers
337
views
1
answers
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 6 months ago by wcstcyx30
0
votes
1
answers
337
views
1
answers
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 6 months ago by wcstcyx30
0
votes
1
answers
337
views
1
answers
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 6 months ago by wcstcyx30
0
votes
2
answers
247
views
2
answers
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 6 months ago by wcstcyx30
0
votes
2
answers
247
views
2
answers
Comment: C: Any way to proceed duplicate removal for list of GRanges object ?
... Hi Jurat, I do not have the ability to delete one of my answer. Maybe the administrators can help us do that. I have made the things happen. Please let me know why lazyFun() is not efficient? In speed or in memory or in number of lines of the code? You have three different tasks. So each one need ...
written 6 months ago by wcstcyx30

Latest awards to wcstcyx

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 359 users visited in the last hour