User: arendsee

gravatar for arendsee
arendsee10
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10
Status:
New User
Location:
Iowa State University
Website:
https://github.com/are...
Last seen:
9 months ago
Joined:
9 months, 2 weeks ago
Email:
a*******@iastate.edu

Posts by arendsee

<prev • 7 results • page 1 of 1 • next >
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Comment: C: CDS phase information missing from GenomicFeatures
... Thanks, the modification to `cdsBy` certainly help. I coded around the partial models in my project by loading the GFF into a GRanges object and adding the phase to the start position (which makes in-frame models). Then I encoded the the original GFF phase in the CDS 'name' field before passing the ...
written 9 months ago by arendsee10
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Comment: C: CDS phase information missing from GenomicFeatures
... The phase will be 0 if the models are complete, but this isn't always the case. Note that the first CDS begins on the very first nucleotide of the scaffold. The GFF example was produced by the AUGUSTUS gene model predictor, which will detect models even when they are broken across scaffolds. I have ...
written 9 months ago by arendsee10
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Comment: C: How to produce png files from printGraph
... Yes, but I can't run the code. No one else can either. The variables 'sampleGOdata', 'resultKS.elim', and 'comparison' are not defined. I had to look up the topGO vignette to find the definitions of 'sampleGOdata' and 'resultKS.elim'. But still I don't know what 'comparisons' is. How is 'comparisons ...
written 9 months ago by arendsee10
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Comment: C: How to produce png files from printGraph
... In your code, you need to declare the variables 'sampleGOdata', 'resultKS.elim', and 'comparisons'. Also you need to include all import statements (e.g. 'library(topGO)'). You should be able to just paste the code example into an R shell and have it run. ...
written 9 months ago by arendsee10
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Comment: C: How to produce png files from printGraph
... Although, your example isn't quite complete. I don't know offhand what package `showSigOfNodes` is from, so I can't immediately replicate your code. You should add the import statements (e.g. `library(whatever)`). I assume that `printGraph` is producing a figure of some sort? ...
written 9 months ago by arendsee10
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Answer: A: How to produce png files from printGraph
... Here is a complete example: library(topGO) library(ALL) data(geneList) sampleGOdata <- new("topGOdata", description = "Simple session", ontology = "BP", allGenes = geneList, geneSel = topDiffGenes, nodeSize = 10, an ...
written 9 months ago by arendsee10
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CDS phase information missing from GenomicFeatures
... The GenomicFeatures library allows gene models to be stored in an SQLite database. Here is the full SQLite schema CREATE TABLE chrominfo ( _chrom_id INTEGER PRIMARY KEY, chrom TEXT UNIQUE NOT NULL, length INTEGER NULL, is_circular INTEGER NULL ); CREATE TABLE transcript ( _tx_ ...
genomicfeatures gff gene models phase written 9 months ago by arendsee10 • updated 9 months ago by Hervé Pagès ♦♦ 13k

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