-
Notifications
You must be signed in to change notification settings - Fork 1
Preprocessing
brakitsch edited this page Dec 9, 2015
·
2 revisions
Before getting started, we have to compute the sample-to-sample genetic covariance matrix:
./gNetLMM_preprocess --compute_covariance --plink_path plink_path --bfile bfile --cfile cfile
where
- plink_path (default: plink) is a pointer to the plink software (Version 1.9 or greater must be installed). If not set, a python covariance reader is employed. We strongly recommend using the plink reader for large datasets.
- bfile is the base name of of the binary bed file (bfile.bed,bfile.bim,bfile.fam are required).
- cfile is the base name of the output file. The relatedness matrix will be written to cfile.cov while the identifiers of the individuals are written to the file cfile.cov.id.
We use the realized relationship matrix (RRM) as genetic covariance matrix.