cole-trapnell-lab/garnett

cross species cell type transfer

justinesjw opened this issue · 3 comments

Hi,

Thank you for the Garnett it has been very useful.

Is it possible to train the classifier on mouse data and classify cells from human data?

Many thanks,
Justine

Hi Justine,

Glad it's been useful. We have had some success doing this. The main obstacle to trying it is the different gene names. The way I've done it before is make a "mouse-ified" human cds object or vice-versa (basically a mouse data cds with human gene names). Here's some code I've used in the past to generate a mouse-human gene table using biomaRt:

require("biomaRt")
human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl")
genesV2 = getLDS(attributes = c("ensembl_gene_id"), 
                 filters = "ensembl_gene_id", 
                 values = fData(human_cds)$gene , 
                 mart = human, 
                 attributesL = c("ensembl_gene_id"), 
                 martL = mouse, 
                 uniqueRows=T)

Then a bunch of merges should get you a gene table and expression matrix with the right gene names that you can feed into new_cell_data_set.

Hope this helps,
Hannah

Hi Hannah,

Thanks!

However, we realized that getLDS() do not convert all genes.
We were able to convert more genes using this library. :)
http://www.informatics.jax.org/downloads/reports/HMD_HumanPhenotype.rpt

Cheers!
Justine

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