waldronlab / SingleCellMultiModal

Single Cell multimodal data scripts for downloading datasets
https://bioconductor.org/packages/SingleCellMultiModal
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CITEseq breaks with one mode #19

Closed LiNk-NY closed 3 years ago

LiNk-NY commented 4 years ago

Hi Dario, @drighelli

The code here is not robust. The helper function expects two inputs every time. Please fix this and create a pull request. I will apply this to both devel and release so please do not bump the version on the commit.

Offending code:

.cord_blood <- function(ess_list)
{
    names(ess_list$experiments) <- c("scADT","scRNAseq")
    mse <- MultiAssayExperiment::MultiAssayExperiment(experiments=(ess_list$experiments))
    return(mse)
}

Example code that should work:

>  mse <- CITEseq(modes = "scADT*", dry.run=FALSE)
snapshotDate(): 2020-10-02
Working on: scADT_Counts
see ?SingleCellMultiModal and browseVignettes('SingleCellMultiModal') for docume
ntation
loading from cache
Error in names(x@listData) <- value : 
  'names' attribute [2] must be the same length as the vector [1]

Thank you!

LiNk-NY commented 3 years ago

This has been fixed. Thank you.