User: Stefanie Tauber

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

<prev • 19 results • page 1 of 2 • next >
0
votes
0
answers
275
views
0
answers
maxScore calculation for 'log2probratio' and 'prob' type PWMs
... 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 ...
biostrings pwm written 14 months ago by Stefanie Tauber40
0
votes
1
answers
434
views
1
answers
Comment: C: calculate frequency of non-overlapping matches for a motif in a XStringSet
... 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 Tauber40
1
vote
1
answer
434
views
1
answer
calculate frequency of non-overlapping matches for a motif in a XStringSet
... 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 ...
biostrings matchpattern patternmatch written 21 months ago by Stefanie Tauber40 • updated 21 months ago by Hervé Pagès ♦♦ 13k
1
vote
1
answer
481
views
1
answer
retrieving phastConsScores via 'scores' from 'VariantFiltering' shows inconsistency
... 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 ...
variantfiltering phastcons written 2.6 years ago by Stefanie Tauber40 • updated 2.6 years ago by Robert Castelo2.0k
0
votes
3
answers
980
views
3
answers
Comment: C: Transitive overlaps of GRanges object
... What a neat, elegant way :) thanks a lot! ...
written 2.8 years ago by Stefanie Tauber40
0
votes
3
answers
980
views
3
answers
Answer: C: Transitive overlaps of GRanges object
... 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 Tauber40
0
votes
3
answers
980
views
3
answers
Comment: C: Transitive overlaps of GRanges object
... 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 Tauber40
0
votes
3
answers
980
views
3
answers
Comment: C: Transitive overlaps of GRanges object
... Thanks for pointing out the graph perspective. I will consider to reformulate the problem in this context! ...
written 2.8 years ago by Stefanie Tauber40
10
votes
3
answers
980
views
6 follow
3
answers
Transitive overlaps of GRanges object
... 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 ...
granges findoverlaps written 2.8 years ago by Stefanie Tauber40 • updated 2.8 years ago by Hervé Pagès ♦♦ 13k
0
votes
1
answers
613
views
1
answers
Comment: C: Finding mismatches between reads and reference sequence
... Thanks so much for the detailed comment! ...
written 2.9 years ago by Stefanie Tauber40

Latest awards to Stefanie Tauber

Popular Question 14 months ago, created a question with more than 1,000 views. For PhD positions in Computational Biology

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 396 users visited in the last hour