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grimbough / biomaRt

R package providing query functionality to BioMart instances like Ensembl
https://bioconductor.org/packages/biomaRt/
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unused argument (feature_symbol = "external_gene_name") #79

Closed ryf0810 closed 1 year ago

ryf0810 commented 1 year ago

Hi Author,

I'm reproducing the code from one paper, which used scater package.

sce <- load10xSCE(here("data/Organoid123"), dataset = "Organoid123", org = "human", add.anno = TRUE, calc.qc = TRUE, calc.cpm = TRUE, pct.mt = TRUE, pct.ribo = TRUE, cell.cycle = TRUE, sparse = TRUE, bpparam = MulticoreParam(workers = 10), verbose = TRUE)

And I encounter the unused argument error stated in the title. Here the Organoid123 folder contains three files of three samples, barcodes.tsv, genes.tsv and matrix.mtx. I tried to delete this argument in the installed package, however I did not find the corresponding R file that contains useMart() function. Thank you!

ryf0810 commented 1 year ago

OK, its not related to the biomaRt package, sorry!