Obtaining cell metadata incl cell type and subtype annotation (Figure 4)

[lgeistlinger]

Assuming familiarity with R and with the SingleCellExperiment container, all you would need to do is to carry out lines 290-310 here:

subtypeHeterogeneity/vignettes/singlecell.Rmd

Line 290 in 0f275d2

Read the pre-processed 10X data for all tumors as `list` of `SingleCellExperiment`s.

and access the colData of the obtained SingleCellExperiments which includes, among other things, the cell type annotation.

For example here for Tumor T59:

> colData(sces[["T59"]])[,c("Barcode", "subtype", "celltype")]
DataFrame with 13040 rows and 3 columns
                 Barcode     subtype    celltype
             <character> <character> <character>
1     AAACCTGAGCTGCCCA-1         DIF         MYE
2     AAACCTGAGTCATCCA-1         DIF         MYE
3     AAACCTGCAAGCCCAC-1         IMR         MYE
4     AAACCTGCAAGCGCTC-1         DIF         EPI
5     AAACCTGCACGTAAGG-1         DIF         EPI
...                  ...         ...         ...
13036 TTTGTCATCCCTTGCA-1         DIF         MYE
13037 TTTGTCATCCGTACAA-1         DIF         MYE
13038 TTTGTCATCCTCCTAG-1         DIF         EPI
13039 TTTGTCATCGGTCTAA-1         DIF         EPI
13040 TTTGTCATCTAACTCT-1         DIF         MYE

[lgeistlinger]

The cell metadata for each tumor can also be obtained as flat text files here:

• Tumor T59
• Tumor T76
• Tumor T77
• Tumor T89
• Tumor T90