Malte Thodberg

Import of BigWig files with rtracklayer fails under MultiCoreParam

21

I'm seeing a weird bug in in my CAGEfightR package when trying to import BigWigFiles. Here's a reproducible example: ``` # Load the example data library(BiocParallel) library(rtracklayer) library(CAGEfightR) data('exampleDesign') #...

Support for correlations between columns of two matrixes

1

Super useful package! Good old cor can easily calculate correlation between the columns of two matrices, like: cor(iris[,1:2], iris[,3:4]) Petal.Length Petal.Width Sepal.Length 0.8717538 0.8179411 Sepal.Width -0.4284401 -0.3661259 Would it be...

I'm using the Seurat-wrappers `RunHarmony.Seurat`, `RunUMAP2`, `mapQuery`, `knnPredict.Seurat` and `buildReferenceFromSeurat` for doing multi-modal (matched scRNA-Seq & scATAC-Seq) reference mapping with Symphony. I can transfer a single label/column from the metadata...

Have extract_array() accept non-integer dim() outputs

1

Upon a little experimentation, it seems the only thing preventing a big.matrix from the bigmemory package to be used as a Seed inside a DelayedArray is that dim() on a...

Question: Is it possible to rebuild the original input data from an rda object?

5

If i have an rda-object from the rda() function, it is possible to get out the orignial input data? Following the example from the rda() documentation: ``` # Fit RDA...

Cryptic error message from subsetByOverlaps, maybe related to recent update to extractROWS?

2

My CAGEfightR package has recently produced a cryptic error message on the Bioconductor servers, that I cannot myself reproduce: ``` Running examples in ‘CAGEfightR-Ex.R’ failed The error most likely occurred...

The new raw-based Factors are great! However, the `droplevels` method produces a warning. Here's an example using the man page for Factor: ``` library(IRanges) set.seed(123) ir0