User: k.askland

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k.askland20
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Posts by k.askland

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Comment: C: bioconductor packages for importing custom annotation tables into R?
... Hi Martin, I apologize for the delay. I was away from the office. I will see if I can implement the function you provided. Thanks again, Kathleen   ...
written 4.4 years ago by k.askland20
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Comment: C: bioconductor packages for importing custom annotation tables into R?
... Thanks again, Martin. Sorry. It's 1.1M SNPs (rs IDs) with 10,000 gene ontology annotations - the gene in which the SNP resides is/is not annotated to that gene ontology term. ...
written 4.4 years ago by k.askland20
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Comment: C: bioconductor packages for importing custom annotation tables into R?
... Hi Martin, Thanks for your response. The problem I am having is that I am not using the annotation file to annotate a set of SNPs or genes, as is usually the case. I actually want to bring the entire file in  because I want to do some processing on the matrix itself.  I tried to take a look at rhd ...
written 4.4 years ago by k.askland20
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bioconductor packages for importing custom annotation tables into R?
... Hello, I would like to know if there is a bioconductor (or more general R) package that facilitates efficient importing/reading of very large genomic annotation files. I have a custom annotation set of ~10,000 columns for 1.1M BP positions (rows) . The read.table and read.csv options fail because ...
annotation importing written 4.4 years ago by k.askland20 • updated 4.4 years ago by Martin Morgan ♦♦ 23k
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Comment: C: biomaRt SNP (rs ID) -to-HGNC symbol mapping question
... Jim. Thanks again for the suggestion for exporting as gff3. Any chance you know how to modify the 'out' file in order to export as .txt as well? ...
written 4.4 years ago by k.askland20
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output from getBM() function in biomaRt package
... I have been able to use the method suggested in response to my last post (biomaRt SNP (rs ID) -to-HGNC symbol mapping question) as an alternative means to obtaining rsID-HGNC symbol maps.  However, I would ideally like to compare several methods for obtaining gene mapping information for a large set ...
biomart written 4.4 years ago by k.askland20
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Comment: C: biomaRt SNP (rs ID) -to-HGNC symbol mapping question
... Thanks, Jim. I actually just want it in a universally recognizable format so that I can import it into other applications that do not necessarily recognize the .rda format.  And I am very familiar with excel's destruction of HUGO symbols, particularly those that appear to it to be dates.   Thanks ...
written 4.4 years ago by k.askland20
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Comment: C: biomaRt SNP (rs ID) -to-HGNC symbol mapping question
... OK, Jim. This all works well. One 'final' question. I'm not familiar with the objects generated by these procedures and for some reason, I cannot write the output to a text file. I get the following error. rsIDtoHGNCmaps_GRanges2 <- cbind(SNPs = as(grolaps, "DataFrame"), Genes = as(gnolaps, "Dat ...
written 4.4 years ago by k.askland20 • updated 4.4 years ago by Hervé Pagès ♦♦ 13k
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Comment: C: biomaRt SNP (rs ID) -to-HGNC symbol mapping question
... The ranges for gns and gns2 look correct. However, when I run the remaining code to generate the hits and  add the HUGO symbols I get a couple of errors. Not sure if the resulting output is correct: onend <- flank(gns, 5000) otherend <- flank(gns, 5000,FALSE) gns2 <- punion(onend, gns) #** ...
written 4.4 years ago by k.askland20 • updated 4.4 years ago by Hervé Pagès ♦♦ 13k
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Comment: C: biomaRt SNP (rs ID) -to-HGNC symbol mapping question
... oops. just got your update! ...
written 4.4 years ago by k.askland20

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Popular Question 3.4 years ago, created a question with more than 1,000 views. For biomaRt SNP (rs ID) -to-HGNC symbol mapping question

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