User: fruce_ki

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fruce_ki10
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University of Dundee
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fruce_ki
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Kimon Froussios

Post-doc Bioinformatician @ University of Dundee

Posts by fruce_ki

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Not getting the expected answers from GenomicRanges follow/precede
... I did look at the docs repeatedly, though not carefully enough it seems. I focused on the strand orientation bit, which can also have the effect of giving the seemingly opposite answer. Friday evening overtime probably not the best time to be learning new things. So the query precedes or follows th ...
written 5 weeks ago by fruce_ki10 • updated 5 weeks ago by Martin Morgan ♦♦ 20k
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Not getting the expected answers from GenomicRanges follow/precede
...   I'm getting the opposite answer than I would expect. This has nothing to do with getting opposite behaviour between '+' and '-' strand. My problem here is all on the  '+' strand.   # Subject ref <- GenomicRanges::makeGRangesFromDataFrame( structure(list(seqnames = structure(c(1L, 1L, 1L ...
genomicranges written 5 weeks ago by fruce_ki10 • updated 5 weeks ago by Valerie Obenchain ♦♦ 6.3k
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Comment: C: How to preserve the strand of coverage in derfinder::regionMatrix() ?
... I feared as much. That is the conclusion we reached in my lab too. So that's what I'm looking into, indeed. I was hoping there might have been an easier way. Oh well...Thanks! At least now I know I'm not overcomplicating it. ...
written 5 weeks ago by fruce_ki10
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How to preserve the strand of coverage in derfinder::regionMatrix() ?
... I am using derfinder (in region mode) for annotation-free DE. Then I want to match the DE regions to the nearest *upstream* known gene. For this it is important to know which strand the coverage is on. However regionMatrix() produces regions that have no strand information. The result of fullCovera ...
derfinder written 5 weeks ago by fruce_ki10 • updated 5 weeks ago by Leonardo Collado Torres540
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Comment: C: IRanges error from derfinder analyzeChr with custom TxDb?
... Ok, that clears it up quite a bit. Many thanks! ...
written 7 weeks ago by fruce_ki10
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Comment: C: IRanges error from derfinder analyzeChr with custom TxDb?
... So what is the recommended/most efficient usage case? Should I use only one of the two options? Like set the desired cutoff right from the load and unset the cutoffPre?  Or maybe set both to the same value? Or is cutoffPre ignored when the data is already filtered and no subsetting is requested? ...
written 7 weeks ago by fruce_ki10
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Comment: C: IRanges error from derfinder analyzeChr with custom TxDb?
... BINGO! I was passing cutoff=NULL to loadCoverage() in an attempt to disable filtering at that stage (since analyzeChr() also has a cutoffPre) while keeping the output structure in the format recognised by analyzeChr(). Since the function did not complain, I assumed it was a valid value. I now tried ...
written 8 weeks ago by fruce_ki10
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Comment: C: IRanges error from derfinder analyzeChr with custom TxDb?
... I've tried different values for the F cutoff from 0.9 to 0.0005 and all of them crashed. It doesn't seem to depend on the value. ...
written 8 weeks ago by fruce_ki10
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Comment: C: IRanges error from derfinder analyzeChr with custom TxDb?
... Hi Michael, I nuked all of my R and re-installed everything fresh. The error persists. ...
written 8 weeks ago by fruce_ki10
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Comment: C: IRanges error from derfinder analyzeChr with custom TxDb?
... Although I'm using the latest R and Bioconductor available for MacOSX, I noticed your version of derfinder is newer. Is there any chance that you recently fixed something relevant to this? ...
written 8 weeks ago by fruce_ki10

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