Running Error With Integrative Analysis of 10X and snATAC

[tzhu-bio]

Error in runHarmony.default(obj = x.sp, eigs.dims = 1:22, meta_data = x.sp@sample): eigs.dim is missing Traceback:

1. runHarmony(obj = x.sp, eigs.dims = 1:22, meta_data = x.sp@sample)
2. runHarmony.default(obj = x.sp, eigs.dims = 1:22, meta_data = x.sp@sample)
3. stop("eigs.dim is missing")

[guorongxu]

yes, I also got the same error but has no idea what's going on.

[tzhu-bio]

yes, I also got the same error but has no idea what's going on. Hi, did you solve this error?

[bgorissen]

You should call runHarmony with eigs.dim instead of eigs.dims. The example provides the following code:

> library(harmony);
> x.after.sp = runHarmony(
    obj=x.sp, 
    eigs.dims=1:22, 
    meta_data=x.sp@sample # sample index
  );

but this should be:

> library(harmony);
> x.after.sp = runHarmony(
    obj=x.sp, 
    eigs.dim=1:22, 
    meta_data=x.sp@sample # sample index
  );