User: Adriana Munoz

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Adriana Munoz100
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Posts by Adriana Munoz

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an error in HeatPlus package
... Hi, I'm trying to use the HeatPlus package, but I'm getting the following error when I tried to use annHeatmap or annHeatmap 2 functions: usemap1 <- annHeatmap(mat, ann) Error: could not find function "annHeatmap" I have followed the instructions from the manual: source("http://bioconductor.o ...
heatplus written 6.5 years ago by Adriana Munoz100 • updated 6.5 years ago by Dan Tenenbaum8.2k
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Comment: C: BioMart server down yesterday and today? Error
... Hi, Thanks for the link to the archives. I checked their archive, but they didn't mention anything about it. Adriana On Wed, Mar 21, 2012 at 3:10 PM, Dan Tenenbaum wrote: > On Wed, Mar 21, 2012 at 11:56 AM, Adriana Munoz > wrote: > > Hi, > > > > I have been trying to r ...
written 7.7 years ago by Adriana Munoz100
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BioMart server down yesterday and today? Error
... Hi, I have been trying to run new queries and old queries that used to work before, but I have been getting the following error from BiomaRt: Error in value[[3L]](cond) : Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web servi ...
biomart written 7.7 years ago by Adriana Munoz100 • updated 7.7 years ago by Dan Tenenbaum8.2k
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Comment: C: Attribute in snp mart to get SNP function (e.g. synonymous, nonsynonymous) ?
... Hi Steffen, Thanks so much for your help. I tried and it works! This was just to check how many SNPs had both values. I agree, your code using c() works, too. Do you know how to write negation condition or more complex expressions in the in the filter of the getBM command? For example, to ex ...
written 8.0 years ago by Adriana Munoz100
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Comment: C: Attribute in snp mart to get SNP function (e.g. synonymous, nonsynonymous) ?
... Thanks so much for the information you sent. It's very useful. I was trying to run the following code to get SNPs with 'consequence_type' = "SYNONYMOUS_CODING&NON_SYNONYMOUS_CODING" , but I got error messages: d <- getBM(attributes = c('refsnp_id', 'consequence_type_tv'), filters = c('cons ...
written 8.0 years ago by Adriana Munoz100
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Comment: C: Attribute in snp mart to get SNP function (e.g. synonymous, nonsynonymous) ?
... Thanks so much for the information on the use of that filter. I could extract the synonymous SNPs that I needed. Do you know if there is any difference between using single quotes (') and double quotes (") for the labels? Would it be safe to assume that the SNPs that are extracted using the filter ...
written 8.0 years ago by Adriana Munoz100
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Comment: C: Attribute in snp mart to get SNP function (e.g. synonymous, nonsynonymous) ?
... Hi Xavier, Thanks so much for the information. I'll upgrade my R version to R 2.14, then. Cheers, Adriana On Mon, Nov 14, 2011 at 3:16 AM, Xavier de Pedro wrote: > As far as I remember, only available since R 2.14. > Cheers > Xavier > > > On 11/11/11 18:16, Adriana Munoz wrot ...
written 8.0 years ago by Adriana Munoz100
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Comment: C: Attribute in snp mart to get SNP function (e.g. synonymous, nonsynonymous) ?
... Hi Valerie, Thanks for the information. I used the filter you mentioned and it works. I'd like to try the Variant Annotation package that you mentioned to get where my variant is located (coding, non-coding, utr, etc.) , too, but I got the following error message in my Mac: "Warning message: In g ...
written 8.0 years ago by Adriana Munoz100
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Attribute in snp mart to get SNP function (e.g. synonymous, nonsynonymous) ?
... > > > Hello, > > I'd like to ask you if there is an attribute to extract SNP function information from variation datasets in biomaRt such as synonymous, nonsynonymous, etc and > > a related filter. > > I'm using the following rcode: snpmart = useMart("snp", dataset="hsapie ...
snp biomart written 8.0 years ago by Adriana Munoz100 • updated 8.0 years ago by Valerie Obenchain6.7k
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Welcome to the "Bioconductor" mailing list
... Hello, I'd like to ask you if there is an attribute for SNP function class for variation datasets in biomaRt that is equivalent to the field 'function-class' (or fxn-class field) in the dbSNP database (NCBI) and a related filter. I think biomaRt is great and I'd really like to use biomaRt to extra ...
snp biomart written 8.0 years ago by Adriana Munoz100 • updated 8.0 years ago by Ramon Diaz-Uriarte70

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