Moderator: Michael Lawrence

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Posts by Michael Lawrence

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Comment: C: Printing DataFrame with nested DataFrames causes error
... I also forgot about that, thanks for the reminder. Support added. ...
written 12 days ago by Michael Lawrence8.9k
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Comment: C: Printing DataFrame with nested DataFrames causes error
... The display has been fixed in devel. The dropping behavior is already complex enough, so the goal is just consistency with data.frame.   ...
written 14 days ago by Michael Lawrence8.9k
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Answer: A: Printing DataFrame with nested DataFrames causes error
... A fix will soon propagate for the display issue. For the extraction issue, what were you expecting if not a single element list? ...
written 14 days ago by Michael Lawrence8.9k
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Comment: C: S4Vectors masks/breaks regular Matrix functions
... I can't remember why I added those, but there must have been some impetus. Could fix the definition in Matrix and settle on Matrix as being the S4-ified matrix package. But changing Matrix tends to be costly, and it's pretty heavy. Presumably stats4 would have turned out the same but they just stop ...
written 15 days ago by Michael Lawrence8.9k
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Comment: C: S4Vectors masks/breaks regular Matrix functions
... Except that the generics in question derive from functions in the base package, so it would be something like "base4" but probably just call it "generics". Or, we could just make the functions in question S3 generics. ...
written 15 days ago by Michael Lawrence8.9k
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Comment: C: pROBLEMS WITH findOverlapPairs
... Or, he is loading the package, but it's too old. ...
written 17 days ago by Michael Lawrence8.9k
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Comment: C: makeTxDbFromUCSC fails to download refLink table
... As stated in the post above, the table is now called "hgFixed.refLink". ...
written 18 days ago by Michael Lawrence8.9k
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Comment: C: convert a sequence to Ranges object
... It depends on the specific case. In special cases, just do the math directly and pass the endpoints to the IRanges constructor. ...
written 19 days ago by Michael Lawrence8.9k
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Comment: C: plotting proteases digestion points in a protein
... The AAStringSet consists of individual AAString objects. You can pull one out with protein1[[1]] and call matchPattern() on that. The width() accessor will get you the length of the string; no need to dig down deep into the object. I think the last issue is now answered by another thread. ...
written 19 days ago by Michael Lawrence8.9k
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Answer: A: convert a sequence to Ranges object
... PartitioningByEnd(c(Positions, nchar(myseq))) ...
written 19 days ago by Michael Lawrence8.9k

Latest awards to Michael Lawrence

Scholar 14 days ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 19 days ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 19 days ago, created an answer that has been accepted. For A: setdiff for GenomicRanges
Scholar 23 days ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 24 days ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 10 months ago, created an answer that has been accepted. For A: setdiff between GenomicRanges objects keeping metadata
Scholar 10 months ago, created an answer that has been accepted. For A: filter "isSnp" for VCF
Scholar 10 months ago, created an answer that has been accepted. For A: Add main title to ggbio's karyogram
Scholar 10 months ago, created an answer that has been accepted. For A: export.bw produces enormous files (10^5 times bigger than they should be)
Scholar 10 months ago, created an answer that has been accepted. For A: "duplicated" on LogicalList with fromLast = TRUE gives error
Scholar 10 months ago, created an answer that has been accepted. For A: How to extract out wanted IntegerList more elegantly from nested list?
Scholar 10 months ago, created an answer that has been accepted. For A: Operations across Lists of GenomicRanges?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Operations across Lists of GenomicRanges?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: setdiff for GenomicRanges
Scholar 10 months ago, created an answer that has been accepted. For A: Proper way to read in a DataFrame with CharacterList columns that was saved to a
Scholar 10 months ago, created an answer that has been accepted. For A: Collapse/Reduce in GRanges by Metadata Column
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to extract out wanted IntegerList more elegantly from nested list?
Scholar 10 months ago, created an answer that has been accepted. For A: Obsolete use of AC_INIT macro
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to use GenomicRanges to find overlaps by percentage covered of interval
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to find particular types of overlap with GenomicRanges
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: parRapply in BiocParallel ?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Combining two GRangesLists
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Collapse/Reduce in GRanges by Metadata Column
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to find the amino acid codon corresponding to a translated genomic position
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: filter "isSnp" for VCF

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