Moderator: Michael Lawrence

Reputation:
10,570
Status:
Trusted
Location:
United States
Last seen:
1 month ago
Joined:
9 years, 8 months ago
Email:
l***************@gene.com

Posts by Michael Lawrence

<prev • 1,332 results • page 1 of 134 • next >
2
votes
1
answer
52
views
1
answers
Answer: A: VariantAnnotation - subset multi-allele variants
... You need one row per ALT, so just `expand(input)` first. ...
written 5 weeks ago by Michael Lawrence11k
0
votes
3
answers
156
views
3
answers
Comment: C: Extract metadata from GRanges object for every genomic coordinate
... I sent an email to Herve about this 2 years ago but he never replied. It would be nice to do this: ``` gp <- GPos(coverage(gr1, weight="score")) ``` Instead, probably need this: ``` gr <- GRanges(coverage(gr1, weight="score")) gp <- GPos(gr, score=rep(score, width(gr))) ``` ...
written 6 weeks ago by Michael Lawrence11k
0
votes
3
answers
156
views
3
answers
Comment: C: Extract metadata from GRanges object for every genomic coordinate
... Btw, the plyranges package skips the scary RleList intermediate: ``` gr <- compute_coverage(gr1, weight="score") ``` ...
written 6 weeks ago by Michael Lawrence11k
2
votes
3
answers
156
views
3
answers
Answer: A: Extract metadata from GRanges object for every genomic coordinate
... It is not necessary to use data.frame, even taking your general approach. Here is a rough sketch: ``` gr.expanded <- GRanges("chr1", IRanges(min(start(gr1)):(max(end(gr1))-1), width=1L), score=0L) for(n in 1:length(gr.expanded)){ try(gr.expanded$score[n] <- score(gr1)[start(gr1) <= star ...
written 6 weeks ago by Michael Lawrence11k
0
votes
1
answer
351
views
1
answers
Comment: C: rtracklayer export bedGraph cannot be loaded into UCSC
... Please note that the GRanges (and IRanges) convention is that ranges are 1-based, inclusive. rtracklayer just follows that convention. ...
written 7 weeks ago by Michael Lawrence11k
0
votes
1
answer
64
views
1
answers
Answer: A: negative AD value interfering with readVcfasVRanges
... Best to ask the maintainer of whatever generated the VCF file. ...
written 8 weeks ago by Michael Lawrence11k
0
votes
1
answer
78
views
1
answers
Answer: A: Assesing genomic segment enrichment with GenomicRanges (R-package)
... To treat ranges as sets, look at the Ranges methods for `setdiff()`, `intersect()` and `union()`. ...
written 10 weeks ago by Michael Lawrence11k
2
votes
2
answers
113
views
2
answers
Answer: A: DataFrame after splitting and back
... In devel there is a new `recursive=TRUE` argument on `expand()` that if `FALSE` will expand columns in parallel, so you can now do: ``` expand(df2, recursive=FALSE) ``` as long as you don't care that the data are sorted by "k". ...
written 3 months ago by Michael Lawrence11k
0
votes
1
answer
112
views
1
answers
Comment: C: How to tell a GAlignmentsList singleton is mate1 or mate2
... Could use the flag utilities like `bamFlagAsBitMatrix()` and `bamFlagTest()`. ...
written 4 months ago by Michael Lawrence11k
0
votes
2
answers
157
views
2
answers
Comment: C: Aggregating scores of multiple metadata columns from one GRanges object on anoth
... I edited by answer to include the call to `bindROWS()` but I'm not sure if it will work. Please provide a fully reproducible example. ...
written 4 months ago by Michael Lawrence11k

Latest awards to Michael Lawrence

Scholar 4 weeks ago, created an answer that has been accepted. For A: Extract metadata from GRanges object for every genomic coordinate
Scholar 7 months ago, created an answer that has been accepted. For A: Subset GRanges object into new object
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 7 months ago, created an answer that has been accepted. For A: How can I create a GmapGenome that doesn't start at index 1?
Popular Question 7 months ago, created a question with more than 1,000 views. For Job Opening: Computational Biologist @ Genentech Bioinformatics
Scholar 7 months ago, created an answer that has been accepted. For A: Detecting Overlaps within Grange Object
Scholar 7 months ago, created an answer that has been accepted. For A: Features within 2kb window, but with resampling
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How to use GenomicRanges to find overlaps by percentage covered of interval
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Importing Gene Symbols with makeTxDbFromGFF
Scholar 7 months ago, created an answer that has been accepted. For A: How to use GenomicRanges to find overlaps by percentage covered of interval
Scholar 7 months ago, created an answer that has been accepted. For A: DataFrame after splitting and back
Popular Question 7 months ago, created a question with more than 1,000 views. For views on Rle using GRanges object
Scholar 7 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Scholar 7 months ago, created an answer that has been accepted. For A: Detecting Overlaps within Grange Object
Scholar 9 months ago, created an answer that has been accepted. For A: Detecting Overlaps within Grange Object
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 14 months ago, created an answer that has been accepted. For A: Detecting Overlaps within Grange Object
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: setdiff for GenomicRanges
Scholar 14 months ago, created an answer that has been accepted. For A: Features within 2kb window, but with resampling
Scholar 2.1 years ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: unlist a exons GRangeslist object and add a gene name column
Scholar 2.1 years ago, created an answer that has been accepted. For A: Subset GRanges object into new object
Scholar 2.1 years ago, created an answer that has been accepted. For A: Can rtracklayer import tab-delimited BED files with unquoted spaces in fields?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 243 users visited in the last hour