User: maltethodberg

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Posts by maltethodberg

<prev • 49 results • page 1 of 5 • next >
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Future plans for the new GPos class
... In continuation of my previous question (https://support.bioconductor.org/p/104597/), I was wondering about the the plans for the new GPos class. I can see it has already been added to vignette, but also that it is currently being actively worked on (along with the underlying IPos object), with one ...
genomicranges gpos written 5 weeks ago by maltethodberg40 • updated 4 weeks ago by Hervé Pagès ♦♦ 13k
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coverage no longer works on GPos objects?
... After the recent update, it seems coverage no longer works on GPos objects?  library(GenomicRanges) ## Example 2: pos_runs <- GRanges("chrI", IRanges(c(1, 6, 12, 17), c(5, 10, 16, 20)), strand=c("+", "-", "-", "+")) gpos2 <- GPos(pos_runs) coverage(a ...
genomicranges gpos written 7 weeks ago by maltethodberg40
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Comment: C: breakTies for a Hits-object based on value in mcols?
... Thanks! So I guess that means there is no solution using breakTies - although as you write in the edited post, that seems like an obvious functionality for that function to have (The current documentation for breakTies is also a bit unclear). As was unaware of the global=TRUE argument to which.max/ ...
written 9 weeks ago by maltethodberg40
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Comment: C: breakTies for a Hits-object based on value in mcols?
... I get the following error when running this code: ​ > sort(hits, by = ~val, decreasing=TRUE) Error in as.vector(x) : no method for coercing this S4 class to a vector  In any case, doesn't breakTies always choose based on the index value, rather than row order? hits2 <- as(hits, "Hits") bre ...
written 9 weeks ago by maltethodberg40
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breakTies for a Hits-object based on value in mcols?
... Say I have Hits-object along these lines: from <- c(5, 2, 3, 3, 3, 2) to <- c(11, 15, 5, 4, 6, 11) hits <- Hits(from, to, 7, 15, sort.by.query=TRUE) For every hit, I can assign some value: mcols(hits)$val <- c(10, 11, 15, 12, 10, 10) I then want to break all ties, similar to brea ...
s4vectors hits written 9 weeks ago by maltethodberg40 • updated 9 weeks ago by Michael Lawrence9.9k
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interGeneCorrelation and voom
... I'm looking at using interGeneCorrelation to calculate correlation between sets of genes for RNA-Seq data. camera can take weights obtained via voom into account, but I was surprised to see that camera does not actually call interGeneCorrelation to do this. As the interGeneCorrelation function itsel ...
limma voom intergenecorrelation written 3 months ago by maltethodberg40
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Comment: C: limma-trend with random effects and/or array weights
... In line with the original question, which sequence of function calls would you use in that case for combining duplicateCorrelation with voom/voomWithArrayWeights? ...
written 4 months ago by maltethodberg40
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Comment: C: Implementing fast mathematical and statistical operations on genomic variables i
... Interesting! I am using functions operating on RleLists extensively (coverage, slice, Views, viewSums, etc), how will they be affected? ...
written 4 months ago by maltethodberg40
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Comment: C: Plans for multicore block processing in DelayedArray?
... Interesting! Looking forward, in order to unlock most of the features of DelayedArray (better compression + parallel block processing), it's better to use RleMatrix instead of a DataFrame of Rle's? One reason for using a DataFrame of Rle's is that it seems much faster to create than an RleMatrix. W ...
written 4 months ago by maltethodberg40
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Comment: C: Plans for multicore block processing in DelayedArray?
... I am only using in-memory objects at the moment, primarily DataFrame of Rle's wrapped with DelayedArray. I was actually wondering what the difference is between a DelayedArray around a DataFrame compared to an RleMatrix - conceptually they seem very similar? Is one more efficient speed or memory-wis ...
written 4 months ago by maltethodberg40

Latest awards to maltethodberg

Popular Question 8 months ago, created a question with more than 1,000 views. For Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
Supporter 22 months ago, voted at least 25 times.

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