Error in .testForValidKeys(x, keys, keytype, fks) :
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@c3954ee6
Last seen 10 weeks ago
United States

I have a cds object file for which I want to do single cell RNA seq analysis (make UMAP and identify cell types) on using monocle and garnett software. I was trying to check what marker genes are in my cds file.

cds1 <- readRDS('example_cds.RDS') head(colData(cds1)) #shows annotations on each column as: cell (character), size factor (numeric), n.umi (numeric), perc_mitochondrial_umis (numeric), scrublet_score (numeric), scrublet_call (character), num_genes_expressed (integer) head(rowData(cds1)) #shows annotations on each row as: gene_short_name (character), id (character), chromosome (character), bp1 (integer), bp2 (integer), gene_strand (character), num_cells_expressed (integer)

library(org.Mm.eg.db) marker_file_path <- "C:/Users/[my username here]/Downloads/kidney_marker_genes.txt" marker genes list

marker_check <- check_markers(cds1, marker_file_path, db=org.Mm.eg.db, cds_gene_id_type = "SYMBOL", marker_file_gene_id_type = "SYMBOL")

plot_markers(marker_check)

However, I'm getting an error (see attached screenshot) error in value

Do you have any suggestions on how I can troubleshoot this step?

SingleCell AnnotationDbi • 178 views
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@james-w-macdonald-5106
Last seen 1 hour ago
United States

Garnett is not a Bioconductor package, and has its own Google Groups page (that I found by googling 'Garnett R package and reading what the Trapnell group has on their website - a useful skill indeed!). You should direct questions there.

As an aside, you don't need to post screen shots. You can simply highlight the code and copy/paste, and then highlight and click the CODE button. There is actually some instructions when you start to post a question that appear right where you are meant to type!

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