User: maltethodberg

gravatar for maltethodberg
maltethodberg100
Reputation:
100
Status:
Trusted
Location:
UCPH
Last seen:
11 hours ago
Joined:
2 years, 9 months ago
Email:
m************@gmail.com

Posts by maltethodberg

<prev • 62 results • page 1 of 7 • next >
0
votes
0
answers
23
views
0
answers
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 1 day ago by maltethodberg100
0
votes
1
answers
62
views
1
answers
Comment: C: bplapply with progressbar
... Picking up on this answer, is it possible to have bpapply show a progress bar similar to pbapply when using SerialCoreParam? ...
written 3 days ago by maltethodberg100
0
votes
1
answers
117
views
1
answers
Comment: C: DelayedArray seeds: SolidRleArraySeed vs ChunkedRleArraySeed vs DataFrame of Rle
... Thanks for the detailed response! I'm considering updating the CAGEfightR-package from using dgCMatrix to using DelayedArray instead (giving the new addition of parallel processing and quick summaries from DelayedMatrixStats, particularly rowsum). Using RleMatrix seems like the obvious choice for re ...
written 19 days ago by maltethodberg100
0
votes
1
answers
117
views
1
answers
Comment: C: DelayedArray seeds: SolidRleArraySeed vs ChunkedRleArraySeed vs DataFrame of Rle
... Thank you for the detailed explanation. A few follow up question: - Why is it beneficial to store the data as a single Rle in SolidRleArraySeed? Doesn't that limit to the total size of the matrix since it spans all columns? - If you chunk a ChunkedRleArray seed by column, how is that different from ...
written 25 days ago by maltethodberg100
8
votes
1
answer
117
views
1
answer
DelayedArray seeds: SolidRleArraySeed vs ChunkedRleArraySeed vs DataFrame of Rle's
... After reading the vignette for DelayedMatrixStats, I'm confused about the mention of two types of RleArray seeds: SolidRleArraySeed & ChunkedRleArraySeed What's the difference between these two seeds and a simple DataFrame of Rle's as seed? Are there perfomance/memory differences between them? ...
delayedarray delayedmatrixstats written 26 days ago by maltethodberg100 • updated 25 days ago by Peter Hickey440
0
votes
1
answers
535
views
1
answers
Comment: C: Calling coverage on GRanges object yields small negative values
... Sorry for reviving an old thread, but I am having the same issue as described in this question. What's a good way to solve this issue if your downstream analysis depends on not having negative values? cov[cov < 0] <- 0 is pretty slow. Perhaps running round(cov) with some number of digits? ...
written 6 weeks ago by maltethodberg100
2
votes
1
answer
74
views
1
answer
Build GPos from IPos
... It would be great if one could construct a GPos from and IPos, similarly to how one can construct a GRanges from an IRanges: GRanges(seqnames=rep("chr1", 3), ranges=IRanges(start=1:3, width=1)) # Works GPos(seqnames=rep("chr1", 3), ranges=IPos(1:3)) # Doesn't work ...
genomicranges granges gpos written 7 weeks ago by maltethodberg100 • updated 6 weeks ago by Hervé Pagès ♦♦ 13k
2
votes
1
answer
66
views
1
answer
Intra-range transformation on GPos-objects?
... I like the new GPos-class alot, specially since most GRanges methods work without any issue. An exception to this is the "intra-range transformations", even though they still make sense for GPos objects. For example the promoters-function: gpos1 <- GPos(c("chr1:44-53", "chr1:5-10", "chr2:2-5") ...
genomicranges granges gpos written 7 weeks ago by maltethodberg100 • updated 6 weeks ago by Hervé Pagès ♦♦ 13k
0
votes
0
answers
41
views
0
answers
Plotting bed8 with Sushi possible?
... I've been trying to use Sushi to plot a bed8-file, containing the location of a cluster and the location of the cluster "peak" in the thickStart/thickEnd columns: library(Sushi) bed8 <- data.frame(chrom="chr18", chromStart=100, ...
bed sushi written 7 weeks ago by maltethodberg100
0
votes
1
answer
99
views
1
answer
mroast/fry with gene weights for most or all genes
... I’m experimenting with the ability of fry/mroast functions to include gene weights. I have two use cases:   1) Comparing the result of a previous experiment in mouse, with a current experiment in human: Basically I want to see if a previous observed response in mouse is observed in a similar human ...
limma mroast fry written 9 weeks ago by maltethodberg100 • updated 8 weeks ago by Gordon Smyth35k

Latest awards to maltethodberg

Popular Question 7 weeks ago, created a question with more than 1,000 views. For DE for genes with very low counts using limma.
Student 3 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 17 months ago, created a question with more than 1,000 views. For Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
Popular Question 17 months ago, created a question with more than 1,000 views. For Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
Supporter 2.6 years ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 176 users visited in the last hour