Re: Cannot project new individuals onto existing PCs

[Gad Abraham]

Hi,

For project(), you need to give the root name of the PLINK data (not a
directory), similar to how you called flashpca() with 'bedf'.

Hope that helps.

Gad

On 20 November 2017 at 04:59, <zhihu...@g.harvard.edu> wrote:
> Hi,
>
> I am running flashpcaR. After successfully generating loadings with
> flashpca, I want to project individuals in my validation set onto the PCs
> built on training set and get the following error message:
> Error in project_plink_internal(X, loadings, ref_alleles, orig_mean,
> orig_sd, :
> Expecting a string vector: [type=NULL; required=STRSXP].
>
> Here's my code, where fn is the directory where I saved my plink files.
> f <- flashpca(bedf,ndim=10,do_loadings=T)
> P3 <- project(fn, loadings=f$loadings, orig_mean=f$center, orig_sd=f$scale)
>
> Thank you!
>
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