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jackbibby1 / SCPA

R package for pathway analysis in scRNA-seq data
https://jackbibby1.github.io/SCPA/
GNU General Public License v3.0
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error x$Genes: $ operator is invalid for atomic vectors #76

Open INeedCNS opened 1 week ago

INeedCNS commented 1 week ago

Hi, I created my own gene set table as shown below, but I always encountered an error: error x$Genes: $ operator is invalid for atomic vectors. Same error I used the combined_metabolic_pathways.csv you provided. However, it worked correctly with the msigdbr pathways. What should I do?

str(pathways) tibble [33 × 2] (S3: tbl_df/tbl/data.frame) $ Pathway: chr [1:33] "CCL" "CCL" "CCL" "CCL" ... $ Genes : chr [1:33] "Ccl1" "Ccl2" "Ccl3" "Ccl4" ...

scpa_out <- compare_pathways(samples = list(resting, activated), 
                             pathways = pathways)

Using single core processing. Specify 'parallel = TRUE' and `cores = x` arguments for parallel processing

Cell numbers in population 1 = 2328
Cell numbers in population 2 = 4057
- If greater than 500 cells, these populations will be downsampled

error x$Genes: $ operator is invalid for atomic vectors
jackbibby1 commented 1 week ago

Hi,

Can you try running:

scpa_out <- compare_pathways(samples = list(resting, activated), 
                             pathways = list(pathways))

Jack