Moderator: russhh
russhh ♦ 5.1k
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Bioinformatics etc of leukaemia at University of Glasgow
Posts by russhh
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Comment:
C: Tripartite Network Construction
... Could you define what the contents of the three parts of the network should be, please? Is it 1) drugs, 2) genes with direct links to drugs, 3) genes that do not link to drugs but do link to members of 2. Is it just a visual representation of the tripartite-ness of the network that you want, or do y ...
written 3 hours ago by
russhh ♦ 5.1k
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... Your install of numpy is probably pinned against MKL and blas, whereas plink is pinned against openblas (and having MKL/blas and openblas in the same env may cause some problems). There is a way to tell conda to use openblas whereever it wants blas: https://github.com/conda-forge/numpy-feedstock/iss ...
written 3 hours ago by
russhh ♦ 5.1k
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Comment:
C: Gene symbol convert to Entrez ID
... But, to store the data, just use assignment: `gene_data <- AnnotationDbi::select(blah, blah, blah)` ...
written 8 days ago by
russhh ♦ 5.1k
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Comment:
C: Gene symbol convert to Entrez ID
... It returns a data.frame. In R you have to be pretty explicit about which function you are using, and the code above might fail if you have `{dplyr}` (or another package that exports a `select` function / method) loaded. If the above doesn't work, you could try `AnnotationDbi::select()` to make it mo ...
written 8 days ago by
russhh ♦ 5.1k
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... Might be a job for {disk.frame} https://github.com/xiaodaigh/disk.frame ...
written 8 days ago by
russhh ♦ 5.1k
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Comment:
C: Create a heatmap
... Yes you can do this. But if you have analysed the data using something like limma or edgeR, then your differential expression pipeline might already have computed the treatment means. You might be able to skip your averaging step and use precomputed results. ...
written 10 days ago by
russhh ♦ 5.1k
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... Then why not have a single output file name used by each run of your Rscript, and encode the mode-genotype within the file, rather than within the filename? ...
written 10 days ago by
russhh ♦ 5.1k
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... Could you explain in english what you want to do, please (rather than in approximate snakemake syntax). For each barcode, is there a single genotype associated with it? ...
written 10 days ago by
russhh ♦ 5.1k
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... Although this isn't a code review site, do you mind if I rewrite your workflow? I'll add some comments to cover any confusing bits that might be the source of your problem.
I can't tell from your code whether `datapath` looks like "some/path/" or "some/path/some_prefix" (I've assumed the former), a ...
written 12 days ago by
russhh ♦ 5.1k
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... Sorry, how does your R-script know which of the genotypes are to be present in the output file? ...
written 12 days ago by
russhh ♦ 5.1k
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