User: Moiz Bootwalla

Reputation:
50
Status:
New User
Location:
United States
Last seen:
3 years, 6 months ago
Joined:
6 years, 6 months ago
Email:
m**********@gmail.com

Posts by Moiz Bootwalla

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Error selecting Gene Symbol using Entrez ID via Homo.sapiens
... Thanks Jim and Marc. I kind of got a handle of it last night when I started looking at the columns being returned by Homo.sapiens and TxDb and saw that TxDb had just GENEID and not EntrezID in it. I thought they were both the same and did not know about the difference between the two. Thank you Marc ...
written 3.6 years ago by Moiz Bootwalla50
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Error selecting Gene Symbol using Entrez ID via Homo.sapiens
... I am getting a very weird error while trying to select a particular SYMBOL using a GENEID using the Homo.sapiens package. The Entrez ID '6218' maps to the Gene Symbol 'RPS17'. When I try to use the select interface to retrieve the gene symbol for only the above entrez id I get an error but if I comb ...
homo sapiens written 3.6 years ago by Moiz Bootwalla50 • updated 3.6 years ago by Marc Carlson7.2k
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Comment: C: ensemblVEP support for Ensembl API version 78
... Thanks Valerie for adding in support so quickly. I will try updating the packages later today.  It's strange but I restarted my machine and re-ran the above code and everything works fine now. Not sure what I was doing wrong. I just want to run my setup by you to be sure that what I did in setting ...
written 3.8 years ago by Moiz Bootwalla50
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ensemblVEP support for Ensembl API version 78
... Hi, I'm trying to use ensemblVEP with version 78 of the Ensembl API. It seems that the package doesn't support version 78 yet. Are there any plans to include support for version 78 soon? It seems that a new option that was introduced in version 78 of the API is causing ensemblVEP() to fail. Here is ...
ensemblvep written 3.8 years ago by Moiz Bootwalla50 • updated 3.8 years ago by Valerie Obenchain ♦♦ 6.6k
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Comment: C: Cannot retrieve Annotations for a GENEID from Homo.sapiens
... Thank you James. Makes sense now. Best, Moiz ...
written 3.9 years ago by Moiz Bootwalla50
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Cannot retrieve Annotations for a GENEID from Homo.sapiens
... I have a GENEID (100505503) that was obtained from TxDb.Hsapiens.UCSC.hg19.knownGene. I was trying to retrieve the SYMBOL for it using Homo.sapiens. I get the following error: select(Homo.sapiens, keys="100505503", columns=columns(Homo.sapiens), keytype="GENEID") Error in .testForValidKeys(x, ke ...
annotation annotationdbi homo.sapiens written 3.9 years ago by Moiz Bootwalla50 • updated 3.9 years ago by James W. MacDonald48k
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Comment: C: Add data to Vcf Info Field
... Thanks Valerie. This is exactly what I was looking for. ...
written 4.0 years ago by Moiz Bootwalla50
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Add data to Vcf Info Field
... I have a vcf file to which I'm trying to add additional annotations. I wanted to know how I can add additional fields to the Info DataFrame. Is there a helper function that allows me to do so in a straightforward manner or do I need to directly manipulate the Info DataFrame itself? Thanks, Moiz & ...
variantannotation written 4.0 years ago by Moiz Bootwalla50 • updated 4.0 years ago by Valerie Obenchain ♦♦ 6.6k
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Comment: C: problem with 'FDb.InfiniumMethylation.hg19'
... I believe this is a result of not having the BSgenome.Hsapiens.UCSC.hg19 package installed on your system. Try installing the package, loading it into your R session and then running get450k(). It should solve it. Post back if it still does not work. HTH, Moiz On Oct 23, 2012, at 7:19 AM, Tim Tr ...
written 6.0 years ago by Moiz Bootwalla50
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Comment: C: Finding TSS locations
... Hi Tom, Continuing with the previous code snippet, here's how you can create a named vector of TSS locations, where the names are the Entrez IDs. tss.vector <- start(tss) names(tss.vector) <- values(tss)$tx_id That should do it. If you plan on working more with GRanges objects you should sp ...
written 6.3 years ago by Moiz Bootwalla50

Latest awards to Moiz Bootwalla

Popular Question 3.6 years ago, created a question with more than 1,000 views. For Error selecting Gene Symbol using Entrez ID via Homo.sapiens
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Add data to Vcf Info Field

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