Error in step 2: arguments imply differing number of rows
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 35/100
- Issue type
- Bug
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- r
- Domain
- bioinformatics
Research direction
Start with the copykat call and the supplied matrix.mtx.gz, features.tsv.gz, and barcodes.tsv.gz inputs, then reproduce the failure at step 2 annotation with the reported mouse dataset. Compare the dimensions of the gene data and annotation inputs around the 9,346/9,347 row mismatch. Done means identifying the cause of the differing rows and documenting a confirmed fix or input requirement.
Written by the indexing model from the issue text.
Description
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
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- R
- Stars
- 305
- Forks
- 66
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