User: Chris Whelan

gravatar for Chris Whelan
Chris Whelan60
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60
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4 years, 5 months ago
Joined:
6 years, 4 months ago
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w*******@ohsu.edu

Posts by Chris Whelan

<prev • 6 results • page 1 of 1 • next >
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Error in makeOrgPackageFromNCBI
... Hi All, I tried to build an OrgDB package from NCBI for gibbon (nomascus leukogenys) and got the error below. Any thoughts on what the problem might be? I was hoping to annotate chip-seq peaks using ChipPeakAnno and GO annotations; I think there's probably ways for me to do this by hand using my da ...
go orgdb annotate gostats written 4.5 years ago by Chris Whelan60
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Error using Homo.sapiens AnnotationDbi package with GenomicFeatures
... Hi, I'm having trouble using the AnnotationDbi package and was wondering if someone could tell me what I'm doing wrong. I'm trying to use GenomicFeatures to find promoter regions and then use AnnotationDbi to look up the Entrez Gene IDs for those transcripts, but getting an error. If I'm going abou ...
go annotationdbi written 5.0 years ago by Chris Whelan60 • updated 5.0 years ago by Marc Carlson7.2k
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Problem with nearest() in GenomicRanges
... Hi Valerie, Thanks for the update to GenomicRanges; it fixed the problem. Just wanted to confirm that for you and the list. Chris On Jul 31, 2012, at 9:45 AM, Valerie Obenchain wrote: Thanks for sending the test data. This is now fixed in GenomicRanges release 1.8.10 and was fixed in devel a few ...
genomicranges written 5.3 years ago by Chris Whelan60
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Comment: C: Problem with nearest() in GenomicRanges
... Hi Valerie, I get this behavior using only a small subset of my data - attached. I am loading it like this: x.data <- read.table("x_data.txt", header=T, sep="\t") cpg.island.data <- read.table('cpg_islands_head.gff') In doing some more testing, it seems like I get this error if not all of t ...
written 5.3 years ago by Chris Whelan60
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Problem with nearest() in GenomicRanges
... Hi all, I'm having an issue with the nearest() method in GenomicRanges. I've created GRanges from two data frames, from data for a species genome assembly with lots of scaffolds: > xs <- with(x.data, GRanges(seqnames=Scaffold, ranges=IRanges(start=Start, end=Stop), strand=Strand)) > xs GR ...
genomicranges written 5.3 years ago by Chris Whelan60 • updated 5.3 years ago by Valerie Obenchain ♦♦ 6.4k
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occurrence of rGADEM motifs (mattia pelizzola)
... Hi Mattia, I just had to figure out how to access the alignment locations returned by rGADEM also. The object returned by GADEM() contains a list of "motif" objects which then have a slot "alignList" that has a list of "align" objects. To pull out the locations for the second motif, for example, th ...
alignment rgadem motiv written 6.3 years ago by Chris Whelan60

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