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dviraran / SingleR

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
GNU General Public License v3.0
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singleR object data structure #85

Open Zepeng-Mu opened 5 years ago

Zepeng-Mu commented 5 years ago

Hi, thanks for the great tool.

I am wondering where can I find the names of reference in singler[[1]] and singler[[2]]. Also, what is the differences between labels and labels1? It seems that some cells are assigned to different cluster in these two labels due to uncertainty? It would be great if there is a more detailed documentation of the singleR data object. Currently, I feel like there is too much information to navigate through.

Thanks!

dviraran commented 5 years ago

Thanks!

  1. There is an 'about' field in each of them that has this information (i.e. singler[[1]]$SingleR.single$about).

  2. labels1 is before fine-tuning, the first round of correlation.

  3. There is some information in the supplementary files (see the bottom of the main page of the GitHub repository), but you are definitely right. We are working on creating a version for Bioconductor that will be documented better.

Best, Dvir