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dviraran / SingleR

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
GNU General Public License v3.0
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Cell labeling using SingleR in seurat #140

Open ruchikabhat opened 3 years ago

ruchikabhat commented 3 years ago

I am trying to use cell labeling via SingleR with reference dataset available with celldex. library(celldex) dice <- DatabaseImmuneCellExpressionData(ensembl=F)

Here is my R script:

_Include_1 <- readRDS("Include_1.rds") library(celldex) dice <- DatabaseImmuneCellExpressionData(ensembl=F) common <- intersect(rownames(Include_1), rownames(dice)) set.seed(2000) trained <- trainSingleR(dice[common,], labels=dice$label.fine, aggr.ref=F) pred <- classifySingleR(Include1, trained, assay.type=1)

While running this R script, it gives following error:

pred <- classifySingleR(Include_1, trained, assay.type=1) Warning: The following arguments are not used: drop Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'type': Cannot find cells provided

Can anyone help me out how to solve this.

Many thanks and regards, Ruchika

P.S. I have merged some patients filtered matrix data and the run PCA and UMAP on it and then saved it as Include_1.rds.

dviraran commented 3 years ago

Please post issues on https://github.com/LTLA/SingleR