User: my4

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my40
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Posts by my4

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Combining ComplexHeatmap with other plot types
... This was exactly what I was looking for.  Thank you! ...
written 21 months ago by my40
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Combining ComplexHeatmap with other plot types
... I have two plots that I want to place next to each other on a grid.  If they were both ggplot2 plots I'd just do something like this: plot_grid(plot_a,plot_b,ncol=2) using the cowplot package. However, one of my plots I have created using the ComplexHeatmap package.  While the other is created wi ...
ggplot2 complexheatmap written 21 months ago by my40 • updated 21 months ago by Zuguang Gu100
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Comment: C: edgeR: Tagwise dispersion when using offset matrix
... Thank you Gordon.  I'll stop worrying about things I don't understand well enough to worry about. ...
written 2.8 years ago by my40
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Comment: C: edgeR: Tagwise dispersion when using offset matrix
... Thank you both for the help.  I have indeed been using y$offsets rather than offset, but as Gordon says it seems to be working fine.  At least, the co-effecients produced by the fit are consistent with what I would expect if the offsets were being applied, but I will correct the error to be on the s ...
written 2.8 years ago by my40
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edgeR: Tagwise dispersion when using offset matrix
... Hello, I am trying to use edgeR with a custom offset matrix (i.e., a different offset value in the GLM for each gene).  I'm doing something like this:         y = DGEList(counts=toc,group=groups)       design = model.matrix(~groups)       y$offsets = too #Where too is a matrix of the same dimensi ...
edger written 2.8 years ago by my40 • updated 2.8 years ago by Aaron Lun24k
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Comment: C: Using S4Vectors within a package
... To answer my own comment, I worked out that I needed to import the table function from BiocGenerics, not S4Vectors.  so importFrom(BiocGenerics,table).  I worked this out largely through trial and error.  The fact that this wasn't obvious to Martin is writing his answer speaks volumes about how conf ...
written 2.8 years ago by my40
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Comment: C: Using S4Vectors within a package
... Sorry for using the wrong mailing list, I'll submit to the one you suggest in future. I tried adding import(S4Vectors), but still got the same error message after installing and loading my package.  That is, mypackage::test(Rle(1:10)) Error in as.vector(x, mode) : invalid 'mode' argument I then ...
written 2.8 years ago by my40
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Using S4Vectors within a package
... I have a stupidly simple function: test = function(...) { table(...) } If I just copy and paste this code into an R session and then run test(Rle(1:10)) I get the expected result.  However, I'm trying to include this function as part of a package, after installing my package mypackage::test(Rle ...
s4vectors package written 2.8 years ago by my40 • updated 2.8 years ago by Martin Morgan ♦♦ 23k
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Comment: A: Efficiently construct GRanges/IRanges from Rle vector
... For a chromosome length object, when I run this     topData = Rle(sample(1:3,1e8,replace=TRUE))     microbenchmark(GRanges('toyChr',IRanges(start(toyData)-1, width=runLength(toyData), toyData = runValue(toyData)), times = 3) It takes roughly 15 seconds to convert     Unit: seconds               ...
written 2.9 years ago by my40
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Efficiently construct GRanges/IRanges from Rle vector
... I have a Run length encoded vector representing some value at every position on the genome, in order. As a toy example suppose I had just one chromosome of length 10, then I would have a vector looking like library(GenomicRanges) set.seed(1) toyData = Rle(sample(1:3,10,replace=TRUE)) I would lik ...
iranges granges rle written 2.9 years ago by my40

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Popular Question 21 months ago, created a question with more than 1,000 views. For edgeR: Tagwise dispersion when using offset matrix

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