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r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
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Problem in runJaccard in SnapATAC #125

Open Sububioinfo opened 4 years ago

Sububioinfo commented 4 years ago

Hi, I am following this tutoril https://nbviewer.jupyter.org/github/pinellolab/scATAC-benchmarking/blob/master/Real_Data/Buenrostro_2018/run_methods/SnapATAC/SnapATAC_buenrostro2018.ipynb?flush_cache=true In step 19 am getting the following error. help me to solve this problem

Jaccard matrix Step 19

the function failed when do.par=TRUE

x.sp = runJaccard( obj = x.sp, tmp.folder=tempdir(), mat = "bmat", max.var=2000, ncell.chunk=1000, do.par=FALSE, num.cores=10, seed.use=10 );

Error Error in runJaccard(obj = x.sp, tmp.folder = tempdir(), mat = "bmat", : unused arguments (ncell.chunk = 1000, do.par = FALSE, num.cores = 1)

r3fang commented 4 years ago

Hi,

Please follow this instruction: https://github.com/r3fang/SnapATAC/blob/master/examples/10X_brain_5k/README.md

The command runJaccard is disabled in the latest SnapATAC package.

Best -Rongxin