SingleCellExperiment

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Internal error in constructor when sample/feature name is NA

3

Hi, when there is NA in sample or feature names, the constructor throws an error which is hard to interpret. `Error in if (!ok) { : missing value where TRUE/FALSE...

TuomasBorman

version field duplicated in int_metadata after concatenating two SCE objects

4

I don't think this affects the users, but I found out this issue when writing a `cbind` method for a class that inherits from SCE and it caused a unit...

lambdamoses

error when using assay()

1

Hi, I got error every time when I try to get count assay from TENxPBMCData, and it doesn't happen before. Here's my code: ``` # BiocManager::install('TENxPBMCData') # (286 KB) library(TENxPBMCData)...

FionaMoon

`combineCols()` errors when called via `do.call()` with a named list of objects to be combined

5

Please note that this may properly be a bug report for **S4Vectors** or **SumarizedExperiment**, so I'm tagging @hpages, but I encountered it when applying `combineCols()` via `do.call()` to a list...

PeteHaitch

Coercion from *SingleCellExperiment* to *SummarizedExperiment* loses rownames

1

``` r suppressPackageStartupMessages(library(SingleCellExperiment)) example(SingleCellExperiment, echo = FALSE) rownames(sce) [1] "Gene_1" "Gene_2" "Gene_3" "Gene_4" "Gene_5" "Gene_6" #> [7] "Gene_7" "Gene_8" "Gene_9" "Gene_10" "Gene_11" "Gene_12" #> [13] "Gene_13" "Gene_14" "Gene_15" "Gene_16" "Gene_17"...

PeteHaitch

logNormcounts() function doesn't work for my singlecellExperiment object

11

`sce

tf1993614

Double validation of the int_elementMetadata slot

6

Hi, Now that `int_elementMetadata` is [registered as a parallel slot](https://github.com/drisso/SingleCellExperiment/blob/bc220cab41b7112347dda5e094ebb2a9c987fb23/R/internals.R#L101-L103) it will be automatically checked by the validity method for Vector objects so there's no need to [check it again](https://github.com/drisso/SingleCellExperiment/blob/bc220cab41b7112347dda5e094ebb2a9c987fb23/R/validity.R#L4-L6)...

hpages

Methods for splitting SingleCellExperiment objects

5

Is there scope to define a splitColData and splitRowData methods for the SingleCellExperiment class? I am working with a rather large SingleCellExperiment object and I often find myself needing to...

jma1991

cbind() hangs if assays don't match

5

When I try to use `SingleCellExperiment::cbind(sce_obj_1, sce_obj_2)`, the method hangs indefinitely if the assays don't match. In my case, I was trying to merge two sets of cells. Each object...

nathancfox

Mistake Locks R Terminal

1

I notice a few times that if I make a mistake, the error message will be printed immediately but I won't be able to use the terminal for a few...

DarioS