The support.bioconductor.org editor has been updated to markdown! Please see more info at: Tutorial: Updated Support Site Editor

Admin: Martin Morgan

gravatar for Martin Morgan
Martin Morgan ♦♦ 23k
Reputation:
22,520
Status:
Trusted
Location:
United States
Website:
http://bioconductor.org/
Last seen:
12 hours ago
Joined:
13 years, 3 months ago
Email:
m************@gmail.com

Posts by Martin Morgan

<prev • 3,063 results • page 2 of 307 • next >
1
vote
1
answer
137
views
1
answers
Answer: A: How to read variants into R from large dataset using VariantAnnotation
... Two suggestions. Use the `VariantAnnotation::readGT()` function for a more efficient input. Use as the path to the VCF file a `VcfFile()` with `yieldSize=` some number of variant to read in a chunk; process the file in an iterative fashion, maybe using `GenomicFiles::reduceByYield()`, which implem ...
written 8 days ago by Martin Morgan ♦♦ 23k
1
vote
1
answer
64
views
1
answers
Comment: C: Ranges from a fasta file
... Backing up, what is it that you want to do? I had not read your question carefully enough, and though that you had sequences, e.g., of chromosomes, and you wanted to extract sub-sequences, e.g., of small RNAs, whose genomic coordinates you knew. You could for instance add a column to your GRanges o ...
written 8 days ago by Martin Morgan ♦♦ 23k
1
vote
1
answer
64
views
1
answers
Comment: C: Ranges from a fasta file
... A GRanges has `seqnames()` (e.g., chromsomes) as well as `names()` (e.g., exon IDs). You want to ensure that all(seqnames(gr_obj) %in% names(fasta)) ...
written 8 days ago by Martin Morgan ♦♦ 23k
1
vote
1
answer
64
views
1
answers
Comment: C: Ranges from a fasta file
... The method is actually in BSgenome; sorry for not being clear. ...
written 9 days ago by Martin Morgan ♦♦ 23k
1
vote
1
answer
64
views
1
answers
Answer: A: Ranges from a fasta file
... Generally, slots (accessed with `@`) are 'internal business' of the object, and not any of our (user) business. I think you want to use `getSeq()`, like > dna = DNAStringSet(c(a="ATGC", b="TGCA")) > gr = GRanges(c("a:1-2", "b:3-4")) > getSeq(dna, gr) A DNAStringSet insta ...
written 9 days ago by Martin Morgan ♦♦ 23k
2
votes
1
answer
94
views
1
answers
Answer: A: CMD check warning using Bioconductor as a source for the dependencies of an R pa
... One can discover dependencies by discovering the packages available for the platform in question ``` db <- available.packages(repos=BiocManager::repositories(), type = "win.binary") ``` and then finding reverse dependencies ``` deps <- tools::package_dependencies("xcms", db, recursive = TRUE) ...
written 12 days ago by Martin Morgan ♦♦ 23k
0
votes
1
answer
94
views
1
answers
Comment: C: CMD check warning using Bioconductor as a source for the dependencies of an R pa
... provide more detail, e.g., the link to the CRAN check and to your package source. ...
written 12 days ago by Martin Morgan ♦♦ 23k
0
votes
3
answers
99
views
3
answers
Comment: C: mclapply to loop over a GRangesList object
... I don't think that's any faster than ``` mclapply(GRsList, gaps, mc.cores = 4) ``` ? The 'cost' is in creating a `GRanges()` for each element of the list, the cost is paid either internally by `lapply()` or explicitly by `GRsList[[i]]`, and either way distributed across cores. The 'Bioconductor' wa ...
written 16 days ago by Martin Morgan ♦♦ 23k
0
votes
3
answers
99
views
3
answers
Comment: C: mclapply to loop over a GRangesList object
... Then you're looking for `GenomicFeatures::intronsByTranscript()`! ...
written 17 days ago by Martin Morgan ♦♦ 23k
1
vote
3
answers
99
views
3
answers
Answer: A: mclapply to loop over a GRangesList object
... Depending on what your goal is, a fast approach is to 'unlist-apply-relist' ```r gr = unlist(grl) gr$foo = ... relist(gr, grl) ``` Probably describing what you would like to do, in not too much detail, would lead to a more helpful answer. ...
written 17 days ago by Martin Morgan ♦♦ 23k

Latest awards to Martin Morgan

Appreciated 11 weeks ago, created a post with more than 5 votes. For Statistics and Computing in Genome Science (CSAMA) Course Material
Scholar 3 months ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
Scholar 3 months ago, created an answer that has been accepted. For A: Is BiocInstaller::biocLite incompatible with withr::with_makevars?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: error with many packages: "Error : .onLoad failed in loadNamespace() for 'org.Hs
Scholar 4 months ago, created an answer that has been accepted. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Scholar 4 months ago, created an answer that has been accepted. For A: Is BiocInstaller::biocLite incompatible with withr::with_makevars?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Scholar 4 months ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
Scholar 6 months ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Popular Question 8 months ago, created a question with more than 1,000 views. For Updated Bioconductor Package Submission Policy
Scholar 8 months ago, created an answer that has been accepted. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Popular Question 8 months ago, created a question with more than 1,000 views. For BioC 2015 Annual Conference
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: error with many packages: "Error : .onLoad failed in loadNamespace() for 'org.Hs
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Scholar 8 months ago, created an answer that has been accepted. For A: How to get chip information from annotation databases
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Error in GRanges: could not find symbol "recursive" in environment of the generi
Scholar 8 months ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
Scholar 9 months ago, created an answer that has been accepted. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Eliminating repetitive calls to ExperimentHub
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Scholar 9 months ago, created an answer that has been accepted. For A: How to get chip information from annotation databases
Scholar 20 months ago, created an answer that has been accepted. For A: about filtering variants in a VCF file

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 182 users visited in the last hour