User: Leonardo Collado Torres

Reputation:
540
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Trusted
Location:
United States
Website:
http://lcolladotor.git...
Twitter:
fellgernon
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Last seen:
13 hours ago
Joined:
8 years, 2 months ago
Email:
l*******@jhu.edu

Leonardo Collado Torres, Ph. D., Data Scientist
Lieber Institute for Brain Development
Clinical Sciences Division
855 N Wolfe St, Suite 300
Baltimore, MD 21205

Website: http://lcolladotor.github.io/about.html
Blog: http://lcolladotor.github.io/

 

Posts by Leonardo Collado Torres

<prev • 162 results • page 2 of 17 • next >
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Comment: C: Matching columns to sample names
... Hi Ben, I think that it'll be best that you contact the TCGA team regarding searching the gdc_file_id's via their web interface (gdc data portal). I don't know if it's a uppercase vs lowercase issue or how their search portal works.  Regarding the TCGA prostate data in recount2, right now you can ...
written 10 weeks ago by Leonardo Collado Torres540
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Comment: C: Matching columns to sample names
... Hi Dorothy, Please check the posting guidelines and create a new post with a reproducible example & session information. Also, use the DESeq2 tag because this has nothing to do with recount from what I can see. Best, Leonardo ...
written 11 weeks ago by Leonardo Collado Torres540
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Answer: A: Matching columns to sample names
... Hi, There are many id columns in the TCGA recount2 metadata. You can access the metadata using colData(rse) or get the metadata for all TCGA samples with all_metadata() as shown below. We used gdc_file_id to match across different tables. library('recount') m <- all_metadata('tcga') head(m$gd ...
written 12 weeks ago by Leonardo Collado Torres540
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Comment: C: IRanges error from derfinder analyzeChr with custom TxDb?
... I normally set both to the same value when loading and when running analyzeChr(). analyzeChr() will only filter again if `colsubset` is used, which sometimes I need to use and others I don't. So setting the cutoff when loading and when running analyzeChr() saves me the trouble of remembering to use/ ...
written 3 months ago by Leonardo Collado Torres540
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Answer: A: IRanges error from derfinder analyzeChr with custom TxDb?
... Hi, The following code reproduces the problem. library('derfinder') datadir <- system.file('extdata', 'genomeData', package='derfinder') files <- rawFiles(datadir = datadir, samplepatt = '*accepted_hits.bam$', fileterm = NULL) ## Shorten the column names names(files) <- gsub('_acce ...
written 3 months ago by Leonardo Collado Torres540
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Comment: C: IRanges error from derfinder analyzeChr with custom TxDb?
... I'm using Bioc-devel but your version of derfinder and mine are the same in terms of these functions. ...
written 3 months ago by Leonardo Collado Torres540
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Comment: C: IRanges error from derfinder analyzeChr with custom TxDb?
... How did you create  chr4Cov and can you show me the head of it? Thanks. It looks like it has to do with position = NULL.  ...
written 3 months ago by Leonardo Collado Torres540
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Comment: C: IRanges error from derfinder analyzeChr with custom TxDb?
... Hi, The TxDb is not an issue here since the TxDb is used later by analyzeChr(). It looks like the F-stat cutoff might be too high, leaving no regions. But that use case should work. Here I run the example code with a very high F-stat cutoff: ``` > ## Collapse the coverage information > co ...
written 3 months ago by Leonardo Collado Torres540
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Answer: A: Read normalization in derfinder
... Hi Helene, targetSize is the target library size. For example, 80 million reads which you could pass as 80e6. Set it to a number you can interpret later. For example, at LIBD for one of our projects we aimed to sequence 80 million reads. You could set it to 1 million reads to get counts per million ...
written 3 months ago by Leonardo Collado Torres540
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Answer: A: Derinder options (species, annotations style)
... Hi, The documentation you are looking for is in the extendedMapSeqlevels() function. There you'll see that it refers to names(GenomeInfoDb::genomeStyles()) for the species names. > names(GenomeInfoDb::genomeStyles()) [1] "Arabidopsis_thaliana" "Caenorhabditis_elegans" "Canis_familiaris" ...
written 3 months ago by Leonardo Collado Torres540

Latest awards to Leonardo Collado Torres

Scholar 5 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Supporter 7 months ago, voted at least 25 times.
Scholar 8 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Scholar 19 months ago, created an answer that has been accepted. For A: derfinder gets stuck in calculatePvalues
Centurion 19 months ago, created 100 posts.
Scholar 2.4 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Scholar 3.0 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: derfinder: fullCoverage() problems
Scholar 3.1 years ago, created an answer that has been accepted. For A: derfinder: fullCoverage() problems
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