## User: Stefanie Tauber

Stefanie Tauber •

**40**- Reputation:
**40**- Status:
- New User
- Location:
- Germany
- Last seen:
- 1 year, 2 months ago
- Joined:
- 7 years, 8 months ago
- Email:
- s**************@gmail.com

#### Posts by Stefanie Tauber

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• 19 results •
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... Hi,
I just wondered about the maxScore calculation for PWMs of different types ('log2probratio' vs 'prob' as given in the help page of PWM).
I would have assumed that for 'log2probratio' the maxScore is the sum of the column-wise maximum of the PWM. This also holds. In contrast, for 'prob' PWM I w ...

written 14 months ago by
Stefanie Tauber •

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... Hi Herve,
thanks for the comment. This definitely helps. Since I am interested in non-overlapping hits, I would calculate - after the conversion to 'NormalIRangesList' the number of non-overlapping hits by means of the width of the matches and the width of the pattern.
In my case, I have many ( abo ...

written 21 months ago by
Stefanie Tauber •

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... Hi,
I would like to count the number of disjoint matches for a given pattern and character vector where matches are sought. So, basically what gregexpr is doing. However I would like to do this for a set of patterns as well as a set of characters (such as XStringSet).
Right now I just apply gre ...

written 21 months ago by
Stefanie Tauber •

**40**• updated 21 months ago by Hervé Pagès ♦♦**13k**1

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... Hi,
I would like to retrieve phastconsscores for a set of ranges from the package 'phastCons100way.UCSC.hg19'. By default, scores will average the retrieved phastconsscores if more than one position is retrieved. Here I retrieve 10 times two positions. Interestingly, I get different values if I ret ...

written 2.6 years ago by
Stefanie Tauber •

**40**• updated 2.6 years ago by Robert Castelo •**2.0k**0

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... What a neat, elegant way :) thanks a lot!
...

written 2.8 years ago by
Stefanie Tauber •

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... Hi Herve,
I think one way to achieve what I would like to do is as follow:
ov = as.matrix(findOverlaps(gr, gr))
ranges_by_overlap = split(gr[ov[, 2]], ov[, 1])
lapply(ranges_by_overlap, function(x) Reduce(intersect,x))
By doing so, all 'correct' transitive overlaps will have a valid intersecti ...

written 2.8 years ago by
Stefanie Tauber •

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... Hi Herve,
thanks for pointing out the 'with.revmap' argument. I was not aware of that argument.
In the end I would like to have the intersection of ranges for which the transitive overlap holds. I would compute the intersection of those ranges via Reduce(intersect, granges). However, I have troubl ...

written 2.8 years ago by
Stefanie Tauber •

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... Thanks for pointing out the graph perspective. I will consider to reformulate the problem in this context!
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written 2.8 years ago by
Stefanie Tauber •

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... Hi,
I have a GRanges object und would like to retrieve sets of reciprocal overlaps:
library(GenomicRanges)
gr = GRanges(seqnames = rep("chr1",4),
ranges = IRanges(start = c(1,2,3,8),
end = c(12,6,6,10)),
strand = rep("+", 4))
> gr
...

written 2.8 years ago by
Stefanie Tauber •

**40**• updated 2.8 years ago by Hervé Pagès ♦♦**13k**0

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... Thanks so much for the detailed comment!
...

written 2.9 years ago by
Stefanie Tauber •

**40**#### Latest awards to Stefanie Tauber

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14 months ago,
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