User: efoss

efoss0
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2 years, 2 months ago
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3 years ago
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Posts by efoss

<prev • 19 results • page 1 of 2 • next >
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... I'm wondering which statistical test would be appropriate here and also whether any Bioconductor or R packages would be useful: Let's say you think that mouse coat color (black, white or orange) might be influenced by the size of the mouse (and imagine that size is binary, i.e. either big or small ...
written 2.2 years ago by efoss0
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... Thanks very much. I appreciate it.  Eric ...
written 2.8 years ago by efoss0
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... Hi Michael,  That's a big improvement - thanks! One follow up question: In your "any" statement, it looks like you can use "TXNAME" without specifying that "TXNAME" is part of "MmOrganismDbTxs". Why is this?  Thanks again for the help.  Eric ...
written 2.9 years ago by efoss0
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... I have a GRanges object called "MmOrganismDbTxs" that has a CharacterList of UCSC-style names as one of the metadata columns, and I have a vector of UCSC-style names that I'm interested in called "desiredUCnames". I would like to subset my GRanges object to pull out a GRanges object that contains on ...
written 2.9 years ago by efoss0 • updated 2.9 years ago by Michael Lawrence10k
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... Dear Thomas,  Thank you very much. I really appreciate it.  Eric ...
written 2.9 years ago by efoss0
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... 120315 This may be related to a previous question I posted, but if so, I'm still in need of guidance:  I made a Mart object as follows:  Mmmart2 <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl") Now I will use "getBM" to ask for six different sets of attributes ...
written 2.9 years ago by efoss0 • updated 2.9 years ago by Thomas Maurel750
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... Thanks so very much, Robert! That really helps.  Eric ...
written 2.9 years ago by efoss0
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...   I would like to use the "promoters" function in the "GenomicRanges" package to generate "GRanges" objects, but I would like these objects to have "REFSEQ" names rather than UCSC-style names.  This gives me UCSC-style names:  library(OrganismDbi) a1 <- promoters(Mus.musculus) Trying the fol ...
written 2.9 years ago by efoss0 • updated 2.9 years ago by Robert Castelo2.2k
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... Hi Valerie,  That fixed it. Thanks so much for the help.  Eric ...
written 2.9 years ago by efoss0
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... P.S. Here are the some of the length commands you entered using my orgs, which was created as described above:  > length(orgs) [1] 1145 > length(orgs$species) [1] 1145 > length(table(orgs$species)) [1] 1145 > query(orgs, "Homo.sapiens") AnnotationHub with 0 records # snapshotDate(): 20 ...
written 2.9 years ago by efoss0

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