User: bruce.moran

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bruce.moran20
Reputation:
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New User
Location:
Ireland
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1 week, 3 days ago
Joined:
2 years, 4 months ago
Email:
b**********@gmail.com

Posts by bruce.moran

<prev • 7 results • page 1 of 1 • next >
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plotMutationSpectrum Colour By Patient with Multiple Samples
... Hi, I have multiple timepoint samples pre- and post-treatment for several patients. I cannot see a standard way to colour mutation spectrum by a 'group' variable, as opposed to sample or mutation. I have the group in the VRanges object supplied to mutationContext, but cannot force via scale_fill_br ...
somaticsignatures somaticsignatures package plotmutationspectrum written 4 months ago by bruce.moran20 • updated 4 months ago by Julian Gehring1.3k
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Comment: C: Gviz AnnotationTrack id above feature
... Thanks Florian, much appreciated! Bruce. ...
written 7 months ago by bruce.moran20
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Gviz AnnotationTrack id above feature
... Hi, hoping one of the Gviz team can help me with this (mostly so I can thank you for the really flexible package!). Example data: cpgGR <- makeGRangesFromDataFrame(data.frame(chrom = c(1,1), start = c(23884842, 23885682), end = c(23885087, 23886212))) ids <- c("CpG:23", "CpG:49") cpgT ...
annotation gviz gviz-package written 7 months ago by bruce.moran20 • updated 7 months ago by florian.hahne@novartis.com1.5k
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Comment: C: DESeq2 rlog error
... Hi Michael, many thanks for the answer, I will change scripts to reflect. Bruce. ...
written 2.1 years ago by bruce.moran20
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DESeq2 rlog error
... Hi, I have been using DESeq2 for a while, it is a good tool, never had any issues. Now I am getting an error at rlog() using 'fast' which is essential AFAIAC: > rldss<-rlog(ddss, fast=T) Error in rlog(ddss, fast = T) : unused argument (fast = T) I do note that the option is removed from ...
deseq2 written 2.1 years ago by bruce.moran20 • updated 2.1 years ago by Michael Love14k
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Answer: A: Ringo Plots Only Partially Made
... Sorry, just caught the issue, transcriptAnno had no strand info so changing all to "+" removes the error. Apologies. Also this is why to use traceback() =D Bruce. ...
written 2.4 years ago by bruce.moran20
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Ringo Plots Only Partially Made
... Hi, I have been following the standard guides for Starr and Ringo for analysis of my Affy tiling array data. It works well, and I get enriched regions and so forth. I would like to make plots from 'cher' (code chunk number 25: plotCher form Ringo link). I run: plot(chers[[1]], expst_ratio_smooth ...
affy tilingarray ringo starr plot written 2.4 years ago by bruce.moran20

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