ERROR WHILE RUNNING PLINKQC IN RSTUDIO ON WINDOWS

Question

[mnakabuye]

Hello, I am trying to run plinkQC on RStudio in Windows and I am getting the error below

Identification of related individuals
Identification of individuals of divergent ancestry
Registered S3 method overwritten by 'data.table':
  method           from
  print.data.table    
Error in evaluate_check_ancestry(qcdir = qcdir, indir = indir, name = name,  :
  plink --pca output file: C:/Users/HP/AppData/Local/Temp/RtmpkhMIat/data.HapMapIII.eigenvec does not exist.

Kindly assist.

Thank you

Mariam

[twesigomwedavid]

The problem seems to be on the preceding code chunk in the plinkQC tutorial (at https://github.com/meyer-lab-cshl/plinkQC/blob/master/doc/plinkQC.Rmd):

```{r copy files}
system(paste("cp", file.path(package.dir, 'extdata/data.HapMapIII.eigenvec'),
                 qcdir))
```

Windows OS does not seem to like that way of copying files in R. Perhaps using the line below instead can fix the problem?

```{r copy_files}
file.copy(file.path(package.dir, 'extdata/data.HapMapIII.eigenvec'), qcdir)
```