Good day,
The default value of colData is DataFrame(). Not specifying an informative
colData is fine.
countsMini <- matrix(rpois(100, 100), ncol = 10)
colnames(countsMini) <- paste("Cell", 1:10)
rownames(countsMini) <- paste("Gene", 1:10)
SummarizedExperiment(assays = list(counts = countsMini))
Good day,
The package has checking errors which the developers of it need to fix
themselves.
Quitting from lines 114-121 (subtypes.Rmd)
Error: processing vignette 'subtypes.Rmd' failed with diagnostics:
object 'lgg.gbm.subtype' not found
The installation error simply indicates that the package
Good day,
So, is the ultimate solution to manually change everything to the format of
\item{\code{show(x)}:}{
...
} ?
The warnings persist, so it does not seem as though R will revert to allowing
the currently-popular syntax past its check.
--
Dario Strben
Good day,
For a long time, it has been a convention to document S4 methods in the format:
\section{Displaying}{
In the code snippets below, \code{x} is a GRanges object.
\describe{
\item{}{
\code{show(x)}:
Displays the first five and last five elements.
}
}
}
In R Under
Hello,
Ah, yes, the sample names should of course be in the rows - Friday afternoon
error. In the question, I specified "largely the same set of features",
implying that the overlap is not complete. So, the example below will error.
DFL <- DataFrameList(X = DataFrame(a = 1:3, b = 3:1, row.names
Good day,
Is there a function in the S4Vectors API which converts a DataFrameList into a
DataFrame, automatically putting the list names into one of the metadata
columns, analogous to MultiAssayExperiment's wideFormat function? The scenario
is mutliple data sets from different organisations mea
Hello,
Might it instead made possible to set an RNGseed value by specifying one to
bpparam but still get the automated back-end selection, so that it could easily
be set to a particular value in an R package?
--
Dario Strbenac
University of Sydney
Camperdown
Good day,
I maintain an R package which makes use of functions such as bplapply which has
bpparam() as the default. I have received feedback from a beginnre user that
the results change when he knitted his R Markdown document a second time. This
stems from the default constructor of bpparam() w
Hello,
Thanks. It was difficult to pinpoint, but I was able to make a minimal example.
It happens only if SummarizedExperiment is pre-loaded. The difference is 0.2
seconds versus 32 seconds on my modest Windows 10 laptop computer - a 150 times
slowdown. Can you reproduce it?
library(Summarized
Good day,
I created two constructor methods for a generic function. One is for the
default empty constructor and the other is a constructor when any one or more
parameters is specified by the user. The method signatures are:
1. c("missing", "missing", "missing", "missing", "missing", "missing",
Good day,
I have an S4 class with some slots in my Bioconductor package. One of the slots
stores the range of top variables to try during feature selection (the
variables might be ranked by some score, like a t-test). The empty constructor
looks like
setMethod("ResubstituteParams", "missing",
Hello,
Ah, I had a few different uses of MultiAssayExperiment::colData in a particular
function of the package, but one line had only colData without the scoping in
front. I wish that R error messages displayed R file names and line numbers
more often.
--
Da
Good day,
I see a checking failure for ClassifyR for Windows Server 2019 only. The error
is
Error: BiocParallel errors
4 remote errors, element index: 1, 4, 6, 8
6 unevaluated and other errors
first remote error: could not find function "colData"
Is there anything I can change in my code
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