The gene_association.py file allows users to run association tests with a phenotype file immediately after the gene expression has been predicted. It is similar to predict_gene_expression.py, but adds the following arguments:
--phen is the path to the .fam file that contains the phenotype info.
--filter is the path to the .filter file that tells the software which subjects to use.
--geoutput is the path/name to the output file for the gene association results.
Additionally, the --output argument has been changed to --troutput to specify the path for the predicted gene expression levels.
To run the gene_association.py:
-R must be installed
-The script PrediXcanAssociation.R needs to be located in the same directory.
-The R package 'dplyr' must be installed
-The python package 'rpy2' must be installed.
The gene_association.py file allows users to run association tests with a phenotype file immediately after the gene expression has been predicted. It is similar to predict_gene_expression.py, but adds the following arguments:
--phen is the path to the .fam file that contains the phenotype info. --filter is the path to the .filter file that tells the software which subjects to use. --geoutput is the path/name to the output file for the gene association results.
Additionally, the --output argument has been changed to --troutput to specify the path for the predicted gene expression levels.
To run the gene_association.py:
-R must be installed -The script PrediXcanAssociation.R needs to be located in the same directory. -The R package 'dplyr' must be installed -The python package 'rpy2' must be installed.