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navinlabcode / copykat

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Error in step 2: arguments imply differing number of rows #112

Open carbui opened 3 months ago

carbui commented 3 months ago

Hi,

I am running copykat on my single cell data from mouse. It runs with no problems in all the samples except this one, which should be all tumor cells and I can´t understand why. My tumor cells have been previously transduced to express mCherry. Maybe it is a problem in annotating mCherry to the normal genes of the mouse genome?

Thanks for the great package and help!

mat <- readMM("matrix.mtx.gz") genes <- read.table("features.tsv.gz", header = FALSE, stringsAsFactors = FALSE) barcodes <- read.table("barcodes.tsv.gz", header = FALSE, stringsAsFactors = FALSE)

gene_symbols <- genes$V2 cell_barcodes <- barcodes$V1

rownames(mat) <- gene_symbols colnames(mat) <- cell_barcodes

copykat.1T <- copykat(rawmat=mat, id.type="S", ngene.chr=5, win.size=25, KS.cut=0.1, sam.name="1T", distance="euclidean", norm.cell.names="",output.seg="FLASE", plot.genes="FALSE", genome="mm10",n.cores=1)

[1] "running copykat v1.1.0" [1] "step1: read and filter data ..." [1] "32287 genes, 2662 cells in raw data" [1] "filtered out 13 cells with less than 200 genes; remaining 2650 cells" [1] "9485 genes past LOW.DR filtering" [1] "step 2: annotations gene coordinates ..." [1] "start annotation ..." Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows: 9346, 9347