I did LD pruning in PLINK. As a result, I have .bed,.bim,.fam,.log and .nosex files. Now, I am trying to do PCA in eigenstrat.
As I understand, I need a parameter file to run the program. I guess I will just write a name for output file but How can I obtain input files?
By default, --pca extracts the top 20 principal components of the
variance-standardized relationship matrix; you can change the number
by passing a numeric parameter. Eigenvectors are written to
plink.eigenvec, and top eigenvalues are written to plink.eigenval. The
'header' modifier adds a header line to the .eigenvec file(s), and the
'tabs' modifier makes the .eigenvec file(s) tab- instead of
space-delimited. You can request variant weights with the 'var-wts'
modifier, and dump the matrix by using --pca in combination with
I coverted bim/fam/bed files to ped/map files using --recode.
I created a txt file with the following contents. (parfile.txt)
I am trying to run convertf -p /data/myname/parfile.txt but it gives following error:
No command 'convertf' found, did you mean:
I hope that someone can help me.