User: Marlin

gravatar for Marlin
Marlin20
Reputation:
20
Status:
New User
Location:
Last seen:
4 months, 2 weeks ago
Joined:
2 years, 3 months ago
Email:
m******@gmx.cn

"In those days spirits were brave, the stakes were high, men were real men, women were real women, and small furry creatures from Alpha Centauri were real small furry creatures from Alpha Centauri. And all dared to brave unknown terrors, to do mighty deeds, to boldly split infinitives that no man had split before."

Posts by Marlin

<prev • 8 results • page 1 of 1 • next >
0
votes
1
answers
224
views
1
answers
Comment: C: Import gff from character?
... Sorry, Martin, it was my fault, I was using import.gff and thought the arguments are passed to import, your example works for me. Thanks! ...
written 17 months ago by Marlin20
3
votes
1
answer
224
views
1
answer
Import gff from character?
... rtracklayer::import for signature "GFFFile,ANY,ANY" has an argument text, the help page says: ## S4 method for signature 'GFFFile,ANY,ANY' import(con, format, text, version = c("", "1", "2", "3"), genome = NA, colnames = NULL, which = NULL, feature.type = NULL, se ...
rtracklayer gff import.gff3 gtf import written 17 months ago by Marlin20 • updated 17 months ago by Martin Morgan ♦♦ 22k
0
votes
1
answers
1.5k
views
1
answers
Comment: C: converting fasta file into bam file
... I think fasta format and bam format represent totally different things, one is for sequence, the other is for alignment. Could you clarify it? ...
written 17 months ago by Marlin20
0
votes
1
answers
354
views
1
answers
Comment: C: Long elapsed time using `import.gff3` with a toy example
... Martin, always thanks for your incisive help. I installed the BSgenome and BSgenome.Hsapiens.UCSC.hg19 packages and it solved the problem. ...
written 2.0 years ago by Marlin20
3
votes
1
answer
354
views
1
answer
Long elapsed time using `import.gff3` with a toy example
... Dear all, I encountered a really long elapsed time for importing a small toy gff3 file  when using `import.gff3()`, here is what I did: > library(rtracklayer) > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > txdb = TxDb.Hsapiens.UCSC.hg19.knownGene > grl.exons = exonsBy(txdb, by = 'tx' ...
rtracklayer import.gff3 written 2.0 years ago by Marlin20 • updated 2.0 years ago by Martin Morgan ♦♦ 22k
3
votes
1
answer
523
views
1
answer
makeTxDbFromGFF drops genes which have multiple chromosome locations. (with iGenome GTF)
... For a GTF file downloaded from iGenome, say, hg19.gtf, a significant proportion of genes will be dropped without warning when use makeTxDbFromGFF to import it. As I examined those genes in the source GTF file, I believe the genes with multiple chromosome locations (e.g. chr1 and chr2) will be dropp ...
genomicfeatures gtf maketxdbfromgff igenome written 2.1 years ago by Marlin20 • updated 2.1 years ago by Martin Morgan ♦♦ 22k
0
votes
3
answers
912
views
3
answers
Comment: C: Gviz: Plot only exons?
... Hey, I just want to comment a convenient way to do this, for anyone who might look at it. It can be done with:  exon <- exonsBy(TxDb.Hsapiens.UCSC.hg19.knownGene, 'tx')[42] exon_mapped <- GenomicFeatures::mapToTranscripts(exon[[1]],exon) And this is just the intended transformation of the e ...
written 2.3 years ago by Marlin20
0
votes
2
answers
327
views
2
answers
ggbio: untransformed coordinate when using `tracks` function with IRanges or numeric value as `xlim`
... I encountered a problem regard to coordinate transformation when using tracks function in ggbio package. An example is here: # Create a GRanges and plot it normally library(ggbio) gr = GRanges('chr2', IRanges(start = 50, end = 100)) p = ggplot(gr) + geom_rect() p   # However, when it is wrapp ...
ggbio tracks written 2.3 years ago by Marlin20 • updated 2.3 years ago by oswaldo.lorenzo10

Latest awards to Marlin

Autobiographer 2.1 years ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 233 users visited in the last hour