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Vivianstats / scImpute

Accurate and robust imputation of scRNA-seq data
https://www.nature.com/articles/s41467-018-03405-7
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Error in mclapply #6

Closed Cady123 closed 6 years ago

Cady123 commented 6 years ago

Hi!

I'm new to single-cell sequencing data and r programming. When I try to use scImpute to impute my data, I got following problem and not so sure how to carry on. I sincerely hope you could help me out. Thanks!

scImpute::scimpute(count_path = "dataNeed.csv", out_dir = "C:/360Downloads/R_workspace",Kcluster = 9) [1] "reading in raw count matrix ..." [1] "number of genes in raw count matrix 26178" [1] "number of cells in raw count matrix 1529" [1] "inferring cell similarities ..." Error in mclapply(1:J, function(id1) { : 'mc.cores' > 1 is not supported on Windows

Vivianstats commented 6 years ago

Hello Cady123,

The reason behind this problem is that the Windows system does not support the mclapply function (used for parallel computation). You might consider setting ncores to 1 if your dataset is not too large. Otherwise, there seem to be some solutions to use the parallel package on Windows, for example: https://github.com/nathanvan/parallelsugar But I've never tried these solutions before so I'm not sure whether they can solve the problem.