Problem with combineTCR() tutorial

[louise-rb-dupuis]

Dear developers,

I wanted to try out scRepertoire on my data but could not pass the "Combining Contigs into Clones" step whatever I was doing.
Each time I got the error "Error: Make sure the sample and ID labels match the length of the list of data frames (df)."

To make sure I was using the function the right way, I copied-pasted the tutorial :

data("contig_list") 
combined.TCR <- combineTCR(contig_list, 
                           samples = c("P17B", "P17L", "P18B", "P18L", 
                                       "P19B","P19L", "P20B", "P20L"),
                           removeNA = FALSE, 
                           removeMulti = FALSE, 
                           filterMulti = FALSE)

and still I got the same error. I saw that the loaded list from the pacakge was 6 elements long so I tried to remove two samples names to see if it changed anything and it didn't. I downloaded the package from BiocManager and here is my session info :
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base

other attached packages:
[1] scRepertoire_1.4.0 celldex_1.4.0 SingleR_1.8.0 clustree_0.4.4 ggraph_2.1.0
[6] harmony_0.1.0 Rcpp_1.0.10 patchwork_1.2.0.9000 scran_1.22.1 scuttle_1.4.0
[11] ddqcR_0.1.0 viridis_0.6.2 viridisLite_0.4.0 forcats_0.5.1 stringr_1.5.1
[16] dplyr_1.1.4 purrr_1.0.1 readr_2.1.0 tidyr_1.3.0 tibble_3.2.1
[21] tidyverse_1.3.1 ggplot2_3.5.0.9000 SingleCellExperiment_1.16.0 SummarizedExperiment_1.24.0 Biobase_2.54.0
[26] GenomicRanges_1.46.1 GenomeInfoDb_1.30.0 IRanges_2.28.0 S4Vectors_0.32.4 BiocGenerics_0.40.0
[31] MatrixGenerics_1.6.0 matrixStats_0.61.0 SeuratObject_4.1.3 Seurat_4.1.1

I will try downloading scRepertoire from github to see if it changes anything.
Best,
Louise

[louise-rb-dupuis]

With the github version using devtools::install_github("ncborcherding/scRepertoire") it works :)
I will not close the issue yet if you want to look at the BiocManager issue.

[ncborcherding]

@louise-rb-dupuis

Thanks for the follow up - the issue was using an outdated scRepertoire version of 1.4.0. We have changed the built-in data for scRepertoire v > 2. So that is why installing from github worked. You should be also able to install from bioconductor with the 3.18/3.19 release.

Thanks,
Nick