flashPCAR cannot load .fam file

[Nicole Torosin]

I am using flashPCAR on linux OS and R version 3.4.3

My plink files are in the directory I am working in and when typing the following 

gatk <- gsub("\\.bed","",

+ system.file("ext.data","gatk.bed",package = "flashpcaR"))

and then trying to run 

f2 <- flashpca(gatk)

The error is

 Error in flashpca_plink_internal(X, stand_i, ndim, div, maxiter, block_size,  : 

  Error reading file '.fam': No such file or directory

Even though it is definitely there and it is called gatk.fam. 

How would I modify the code to make the path to this file clearer, or is there another solution here?

Thank you for any input!

[Gad Abraham]

Hi Nicole,

The system.file function is only for loading the example data provided with the package. To read you own data, you don't need that.

Try running

f2 <- flashpca("gatk.fam")

and see if that works.

Gad

[Nicole Torosin]

Thank you so much for clarifying Gad, that was helpful. 

I'm also stuck now on how to designate colors for different individuals or populations. I'm not sure where to code the populations, or species in my case, into the plink files and how to then translate that into color coding. Right now each individual is labeled but I cannot see how to translate that either. For example gatk$individual does not work. 

Any advice here would be appreciated, thank you!

Nicole 

[Gad Abraham]

Hi Nicole,

That's more of an R issue than a flashpca question, but you'll
basically need to read that external information (species or whatever
you want to plot by), e.g., using read.table(), making sure it's in
the same exact ordering as the fam file, then when you go to plot the
PCs, use the information from that external source as the colour
specification for the plot.

Hope that helps.
Gad

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[Nicole Torosin]

Hi Gad, 

I really appreciate you helping me with that. One last question, I hope, is there any way to figure out which genetic variants are responsible for PC1 and PC2?

Thank you so much,

Nicole 

[Gad Abraham]

Nicole, these would be the per-SNP loadings, to get these you'll need
to re-run flashpca with do_loadings=TRUE, and then look at
f2$loadings.

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