User: Jeff Johnston

gravatar for Jeff Johnston
Reputation:
90
Status:
Trusted
Location:
United States
Last seen:
1 year, 4 months ago
Joined:
5 years ago
Email:
j*********@cmh.edu

Posts by Jeff Johnston

<prev • 14 results • page 1 of 2 • next >
0
votes
1
answer
381
views
1
answers
Comment: C: breakTies for a Hits-object based on value in mcols?
... It looks like Hits need to stay sorted by query: hits <- sort(hits, by = ~ queryHits + val) breakTies(hits, "last") ...
written 16 months ago by Jeff Johnston90
0
votes
1
answer
583
views
1
answers
Comment: C: Extract coordinates of overlapping genomic intervals
... As the overlaps.gr is a GRanges object, you can use start(), end() and seqnames() to extract the coordinates of the overlapping intervals. ...
written 2.7 years ago by Jeff Johnston90
0
votes
1
answer
583
views
1
answers
Comment: C: Extract coordinates of overlapping genomic intervals
... Yes, it generates the overlapping interval for each row (a query/subject pair) in your Hits object. ...
written 2.7 years ago by Jeff Johnston90
2
votes
1
answer
583
views
1
answers
Answer: A: Extract coordinates of overlapping genomic intevals
... You can use pintersect: overlaps.gr <- pintersect(df1.gr[queryHits(dfs.ol)], df2.gr[subjectHits(dfs.ol)]) If you want all the results in one object, you can add the indices as metadata columns: overlaps.gr$df1_hit <- queryHits(dfs.ol) overlaps.gr$df2_hit <- subjectHits(dfs.ol)   ...
written 2.7 years ago by Jeff Johnston90
0
votes
1
answer
792
views
1
answers
Comment: C: Group GRanges and keep metadata
... Wasn't there talk at some point about modifying Views to support GRanges? That would allow convenient things like this: mcols(H1.chr22)$mean_score <- viewMeans(Views(rle, H1.chr22)) Currently this is a bit of a pain because coercing a GRanges into a RangesList modifies the order. ...
written 2.9 years ago by Jeff Johnston90
2
votes
1
answer
717
views
1
answers
Answer: A: export BSgenome directly in gzipped fasta
... This seems to work: library(BSgenome.Dmelanogaster.UCSC.dm3) export(Dmelanogaster, "dm3.fasta.gz", compress=TRUE)   ...
written 3.0 years ago by Jeff Johnston90
0
votes
1
answer
589
views
1
answers
Comment: C: Is there an easy way to extend coverage to seqlengths and fill with zeroes?
... In the case where you have existing coverage, you can coerce it back to a GRanges and then call coverage again with the desired width argument (or set the seqlengths of the GRanges first): gr <- as(cov, "GRanges") new_cv <- coverage(gr, weight="score", width=your_seqinfo)     ...
written 3.2 years ago by Jeff Johnston90
0
votes
1
answer
570
views
1
answers
Comment: C: updateObject() fails for old serialized GRanges objects
... Thanks Hervè. Here is a link for the object: https://dl.dropboxusercontent.com/u/726183/bioconductor/toll10b_k27ac_2to4h_1.ranges.RData We certainly have the ability to recreate all of these objects under a new version of Bioconductor using the original source data; the serialized GRanges objects a ...
written 4.4 years ago by Jeff Johnston90
3
votes
1
answer
570
views
1
answer
updateObject() fails for old serialized GRanges objects
... We have a number of serialized GRanges objects in RData format that cannot seem to be handled by updateObject() in Bioconductor 3.0. These all seem to have been created with Bioconductor 2.8. The version 2.9 objects appear to be working fine. Here's the output from calling updateObject(): > loa ...
genomicranges written 4.4 years ago by Jeff Johnston90 • updated 4.4 years ago by Hervé Pagès ♦♦ 13k
0
votes
1
answer
677
views
1
answer
Thread safety of BSgenome getSeq()
... Thanks for looking into this Herv? and Martin, and for the quick fix. It is working as expected now. I did have to install the updated packages from source as the binaries do not seem to be updating for Mac or Linux. Thanks, Jeff On Jun 18, 2014, at 1:14 PM, Hervé Pagès wrote: > Hi Jeff, > ...
cancer bsgenome process rsamtools written 4.8 years ago by Jeff Johnston90 • updated 4.8 years ago by Hervé Pagès ♦♦ 13k

Latest awards to Jeff Johnston

Scholar 3.0 years ago, created an answer that has been accepted. For A: export BSgenome directly in gzipped fasta
Scholar 3.0 years ago, created an answer that has been accepted. For A: export BSgenome directly in gzipped fasta

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 171 users visited in the last hour