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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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undefined columns selected #126

Open rahulnutron opened 4 years ago

rahulnutron commented 4 years ago

Hello! Thanks for the tool!

I was trying to use the tool for a Arabidopsis scRNA-seq data. I load the matrix, however I think for 'annot' format I am getting a error. I will be thankful for any help!

Regards, Rahul

anno_tb<-read.csv("E:/testscpred1.csv",row.names = 1) head(anno_tb) Cell_type AAACCTGAGAATTCCC-1 Columella AAACCTGAGGGCACTA-1 Columella AAACCTGAGTAATCCC-1 Columella AAACCTGAGTACGTTC-1 Columella AAACCTGAGTATTGGA-1 Columella AAACCTGCAAAGGAAG-1 Columella

singler = CreateSinglerSeuratObject(counts = "E:/Zhang/root_atlas/root_matrix/TAIR/matrix.mtx", annot = "E:/testscpred1.csv", project.name = 'Ara', min.genes = 500, min.cells = 2, npca = 10, regress.out ='nUMI', technology= 'C1', species = 'Arabidopsis', citation = 'Zhang et al. 2019',reduce.file.size = T, variable.genes = 'de', normalize.gene.length = T) [1] "Ara" [1] "Reading single-cell data..." Error in [.data.frame(types, , 1) : undefined columns selected

dviraran commented 4 years ago

Please use the new SingleR version on bioconductor - https://bioconductor.org/packages/release/bioc/html/SingleR.html.