Open linhuawang opened 1 year ago
I tried to apply COPYKAT on a Visium Spatial Transcriptomics dataset from SpaceRanger output. However, I got the following error message:
[1] "step 5: segmentation..." Error in seq.default(1, as.integer(n/bins - 1) * bins, bins) : wrong sign in 'by' argument
Here is my code:
data_folder = '/mnt/atlas_local/linhua/data/RESORT_package/test/data/VisiumData/EMT/filtered_feature_bc_matrix/' raw <- Read10X(data.dir = data_folder) raw <- CreateSeuratObject(counts = raw, project = "copycat.test", min.cells = 10, min.features = 0) exp.raw <- as.matrix(raw@assays$RNA@counts) copykat.test <- copykat(rawmat=exp.raw, id.type="S", ngene.chr=1, win.size=15, KS.cut=0.1, sam.name="test", distance="euclidean", norm.cell.names="", output.seg="FLASE", plot.genes="TRUE", genome="hg20",n.cores=5)
And here is the complete log:
[1] "running copykat v1.1.0" [1] "step1: read and filter data ..." [1] "14082 genes, 2598 cells in raw data" [1] "10405 genes past LOW.DR filtering" [1] "step 2: annotations gene coordinates ..." [1] "start annotation ..." [1] "step 3: smoothing data with dlm ..." [1] "step 4: measuring baselines ..." number of iterations= 1695 number of iterations= 34 number of iterations= 3 [1] "step 5: segmentation..." Error in seq.default(1, as.integer(n/bins - 1) * bins, bins) : wrong sign in 'by' argument
ngene.chr is set to be 1 because any value >1 resulted in all cells (spots) being filtered.
Any suggestion is appreciated!
I tried to apply COPYKAT on a Visium Spatial Transcriptomics dataset from SpaceRanger output. However, I got the following error message:
Here is my code:
And here is the complete log:
ngene.chr is set to be 1 because any value >1 resulted in all cells (spots) being filtered.
Any suggestion is appreciated!