User: efoss

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efoss0
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Posts by efoss

<prev • 19 results • page 1 of 2 • next >
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What statistical test is appropriate? 2 categorical independent variables, 3 categorical dependent variables, biological replicates
... 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 ...
genetics written 15 months ago by efoss0
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Comment: C: subsetting a GRanges object with IntegerList and CharacterList metadata columns
... Thanks very much. I appreciate it.  Eric ...
written 23 months ago by efoss0
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Comment: C: subsetting a GRanges object with IntegerList and CharacterList metadata columns
... 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 23 months ago by efoss0
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subsetting a GRanges object with IntegerList and CharacterList metadata columns
... 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 ...
genomicranges granges written 23 months ago by efoss0 • updated 23 months ago by Michael Lawrence9.8k
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Comment: C: seemingly erratic responses to different getBM biomaRt requests depending on the
... Dear Thomas,  Thank you very much. I really appreciate it.  Eric ...
written 23 months ago by efoss0
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seemingly erratic responses to different getBM biomaRt requests depending on the attributes requested
... 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 ...
biomart getbm written 23 months ago by efoss0 • updated 23 months ago by Thomas Maurel700
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Comment: C: using the "promoters" function with an "OrganismDb" to generate "GRanges" with "
... Thanks so very much, Robert! That really helps.  Eric ...
written 24 months ago by efoss0
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using the "promoters" function with an "OrganismDb" to generate "GRanges" with "REFSEQ" rather than UCSC gene names
...   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 ...
organismdb granges ucsc promoter refseq written 24 months ago by efoss0 • updated 24 months ago by Robert Castelo2.0k
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Comment: C: Why are important organisms missing from AnnotationHub() $rdataclass == "OrgDb"?
... Hi Valerie,  That fixed it. Thanks so much for the help.  Eric ...
written 24 months ago by efoss0
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Comment: C: Why are important organisms missing from AnnotationHub() $rdataclass == "OrgDb"?
... P.S. Here are the some of the length commands you entered using my orgs, which was created as described above:  > length(orgs) [1] 1145 > length(orgs$species) [1] 1145 > length(table(orgs$species)) [1] 1145 > query(orgs, "Homo.sapiens") AnnotationHub with 0 records # snapshotDate(): 20 ...
written 24 months ago by efoss0

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