User: dondelelcaro

gravatar for dondelelcaro
dondelelcaro10
Reputation:
10
Status:
New User
Location:
USA/Champaign/University of Illinois
Website:
http://www.donarmstron...
Twitter:
dondelelcaro
Last seen:
10 months, 2 weeks ago
Joined:
1 year ago
Email:
d**@donarmstrong.com

Posts by dondelelcaro

<prev • 7 results • page 1 of 1 • next >
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Comment: C: GRanges nearest fails for non-overlapping regions
... OK, I'm still not sure what is causing this, but rebuilding S4Vectors and BiocGenerics fixes the issue. The difference that I can tell is:   > which(Rle(c(TRUE,FALSE),c(5,3))) Error in base::which(x, arr.ind, useNames, ...) : argument to 'which' is not logical > showMethods("which") Func ...
written 10 months ago by dondelelcaro10
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Comment: C: GRanges nearest fails for non-overlapping regions
... Looks like I can reduce this to: > library("S4Vectors") Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clu ...
written 10 months ago by dondelelcaro10
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Comment: C: GRanges nearest fails for non-overlapping regions
... R version 3.3.2 (2016-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux stretch/sid locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 ...
written 10 months ago by dondelelcaro10
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GRanges nearest fails for non-overlapping regions
... GenomicRanges::nearest fails because strand(subject) != "-" is not logical: > nearest(GRanges(seqnames=Rle("1",1),ranges=IRanges(start=1,end=10)),GRanges(seqnames=Rle("1",1),ranges=IRanges(start=100,end=120))) Error in base::which(x, arr.ind, useNames, ...) :   argument to 'which' is not logical ...
genomicranges granges bug nearest written 10 months ago by dondelelcaro10
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Answer: A: Pathview: Exporting non native KEGG pathway to PNG
... If you use the patch that I just created (https://github.com/dondelelcaro/pathview) you can call png() before calling pathview(...,write.plot=FALSE) if that's helpful. ...
written 12 months ago by dondelelcaro10
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pathview should support not creating new devices
... pathview() currently always writes a new pdf or png, which makes it rather hard to integrate into knitR and other workflows. This patch allows for using the current graphical device instead of writing to a file.   See https://github.com/dondelelcaro/pathview/tree/feature/add_write.plot ...
pathview written 12 months ago by dondelelcaro10
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GSEABase getGmt() fails when more than 1 line contains duplicates
... > temp <- getGmt("Human_NetPath_September_01_2016_Entrezgene.gmt",geneIdType=EntrezIdentifier()) Error in doWithOneRestart(return(expr), restart) : bad error message the failure is because .warningf() is called with more than one string as its second argument. Changing R/getObjects.R with th ...
gseabase bug written 12 months ago by dondelelcaro10 • updated 12 months ago by Martin Morgan ♦♦ 20k

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