User: maltethodberg

gravatar for maltethodberg
maltethodberg140
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140
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Sweden
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Posts by maltethodberg

<prev • 71 results • page 1 of 8 • next >
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Checking if to DataFrames are identical
... I'm trying to check if to DataFrame objects are identical. My case in point: > d1 DataFrame with 3 rows and 4 columns Name BigWigPlus BigWigMinus totalTags C547 C547 mm9.C547.plus.bw mm9.C547.minus.bw 12436172 C54 ...
s4vectors dataframe written 3 months ago by maltethodberg140
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Answer: A: Genome database and transcription database have different lengths
... You are correct, CAGEfightR is complaining that the two genomes (obtained via seqinfo()/seqlengths() ) are not identical. I have seen a couple of people having similar problems, so CAGEfightR is probably currently a bit too strict in enforcing this. We will probably remove this error in future versi ...
written 4 months ago by maltethodberg140
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Comment: C: CAGEFightR to get CTSS from CAGE error
... This could be an issue with the BigWig-input files. CAGEfightR assumes all ranges in the BigWig is exactly 1, i.e. a single count for each single basepair (traditional CTSS format). This could be checked using something like this: `gr <- import(bw_file)` `table(width(gr))` ...
written 7 months ago by maltethodberg140
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Comment: C: Adding a legend to a GeneRegionTrack?
... The use case was manually setting colors of items on a GeneRegionTrack, for example colouring by strand. I figured a somewhat hacky workaround: You can use an OverlayTrack, to put a DataTrack with no data but a legend on top of a GeneRegionTrack. You have to do some fiddling to make sure the feature ...
written 8 months ago by maltethodberg140
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Adding a legend to a GeneRegionTrack?
... Quick Gviz question: For a DataTrack, there is an option to add a legend via setting legend=TRUE I'm using the feature argument in GeneRegionTrack to color different features. Is there a way to add a legend to the track indicating what the colors mean? Simply supplying legend=TRUE does not work. ...
gviz generegiontrack written 9 months ago by maltethodberg140
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What's the recommended way to overwrite the seqinfo of a GRanges?
... I'm having some difficulties when using rtracklayer to import BigWig-files: import.bed includes the genome argument, which correctly sets the seqinfo on the resulting GRanges. However, import.bw does not have a similar argument; The resulting GRanges will have the seqinfo stored in the BigWigFile. ...
rtracklayer granges import.bw seqinfo bigwigfile written 9 months ago by maltethodberg140 • updated 9 months ago by Michael Lawrence11k
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Comment: C: Correct use of Nested/Stage-wise testing with limma/stageR for 3-group design.
... Thanks for the detailed comment! I don't think the the two-stage approach you suggest would be entirely appropriate here, as the two timepoints have a very different number of pairwise differences (more than twice as many difference between sites on the segment time point). Would it still be correc ...
written 10 months ago by maltethodberg140
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Correct use of Nested/Stage-wise testing with limma/stageR for 3-group design.
... I'm analysing an RNA-Seq dataset with the following study design: Three locations (e.g. A, B, C) at two different times (e.g. time 1 and 2), everything in triplicates. I'm interested in finding DE genes within each time point: A1 vs B1, A1 vs C1, B1 vs C1, and similarly for the second time point. I ...
limma decidetests stager written 11 months ago by maltethodberg140 • updated 11 months ago by Koen Van den Berge170
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Comment: C: Best way of creating a large RleMatrix
... Thank you! Does the new constructor affect how the chunks are structured? If you construct an RleMatrix from a DataFrame of Rle's, is the RleMatrix then chunked by column? ...
written 11 months ago by maltethodberg140
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Best way of creating a large RleMatrix
... What's the preferred way of creating a large RleMatrix? The documentation page ?RleMatrix only covers how make an RleMatrix from a single Rle (which doesn't work for very large RleMatrix objects) First creating a normal matrix and then coercing to RleMatrix, requires keeping the original matrix in ...
delayedarray rlematrix written 13 months ago by maltethodberg140 • updated 11 months ago by Hervé Pagès ♦♦ 14k

Latest awards to maltethodberg

Scholar 4 months ago, created an answer that has been accepted. For A: Genome database and transcription database have different lengths
Voter 11 months ago, voted more than 100 times.
Popular Question 13 months ago, created a question with more than 1,000 views. For DE for genes with very low counts using limma.
Popular Question 14 months ago, created a question with more than 1,000 views. For DE for genes with very low counts using limma.
Student 16 months ago, asked a question with at least 3 up-votes. For Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE methods?
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
Supporter 3.6 years ago, voted at least 25 times.

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