User: Charles Plessy

Reputation:
90
Status:
Trusted
Location:
Japan
Last seen:
1 week, 1 day ago
Joined:
3 years, 4 months ago
Email:
c***********@plessy.org

Posts by Charles Plessy

<prev • 30 results • page 1 of 3 • next >
0
votes
1
answers
103
views
1
answers
Comment: C: bam2CTSS function error from CAGEr package
... Perhaps you need to restart in a fresh R session so that the upgrade of MultiAsssayExperiment and SummarizedExperiment has its effect. ...
written 8 days ago by Charles Plessy90
0
votes
1
answers
103
views
1
answers
Comment: C: bam2CTSS function error from CAGEr package
... Judging from their version numbers, the SummarizedExperiment and MultiAssayExperiment packages seem quite outdated on your system. Can you update them to the current Bioconductor release ? ...
written 9 days ago by Charles Plessy90
0
votes
1
answers
103
views
1
answers
Comment: C: bam2CTSS function error from CAGEr package
... As explained in point 3.1 of the vignette, you also need: library("MultiAssayExperiment") library("SummarizedExperiment") ...
written 9 days ago by Charles Plessy90
0
votes
1
answers
52
views
1
answers
Comment: C: no import.bam function in CAGEr version 1.22.3
... Can you mark the questions as answered if your problems were solved ?  This will help me to track the open issues.  Thanks ! ...
written 9 days ago by Charles Plessy90
0
votes
1
answers
103
views
1
answers
Comment: C: bam2CTSS function error from CAGEr package
... Please do not use the import.bam function directly: it is a private function that is not exported in the namespace, and is not intended for direct use.  Instead, create a CAGEr object as explained in the package's vignette.  In case you do not need the complexity of a CAGEr object, have a look at mo ...
written 9 days ago by Charles Plessy90
0
votes
1
answers
52
views
1
answers
Comment: C: no import.bam function in CAGEr version 1.22.3
... Hi, this function (and a bunch of others) are "private" in the sense that they are not exported and not expected to be directly useful to most users.  Sorry that the documentation is not clear about this.  You can also call it by prefixing its name with the package name (CAGEr:::import.bam).  In any ...
written 9 days ago by Charles Plessy90
0
votes
0
answers
59
views
0
answers
Comment: C: CAGEr: consensusCluster doesn't have dominant CTSS info
... Thanks Jingwen, I will correct this. By the way, I am also tracking this issue on GitHub: https://github.com/charles-plessy/CAGEr/issues/1. If you would like to submit a patch you are very welcome ! ...
written 4 months ago by Charles Plessy90
0
votes
1
answers
344
views
1
answers
Answer: A: CAGEr - How to change plot axis range in CAGEr
... Hi Tobias, plotInterquantileWidth has a a xlim parameter that takes a pair of values representing the boundaries of the histogram to be plotted.  In your case for instance, you would need to pass xlim = c(0,100). ...
written 5 months ago by Charles Plessy90
2
votes
1
answer
208
views
1
answer
Build error: could not find function "bplapply"
... The current version (1.21.4) of the CAGEr package fails to check with the following error: * checking examples ... ERROR Running examples in ‘CAGEr-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: CustomConsensusClusters & ...
biocparallel build report written 9 months ago by Charles Plessy90 • updated 9 months ago by Martin Morgan ♦♦ 22k
0
votes
1
answers
460
views
1
answers
Comment: C: What is the proper way to modify mcols of a GRanges inside a GRangesList?
... As of today, I do not manage to reproduce the examples above.  After running example("GRangesList") to create a grl object with "score" and "GC" mcols, here is what I get: > grl[,"newColumn"] <- "new value" Error in `[<-`(`*tmp*`, , "newColumn", value = "new value") : replacement value ...
written 9 months ago by Charles Plessy90

Latest awards to Charles Plessy

Scholar 16 months ago, created an answer that has been accepted. For A: CAGEr BAM files size issue
Supporter 2.6 years ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 336 users visited in the last hour