PyGenePlexus with R

PyGenePlexus can be run in R using the reticulate pacakge.

# Load the libraries
library(reticulate)
# Path to python environment with PyGenePlexus installed
use_python("PATH/TO/PYTHON")
geneplexus <- import("geneplexus")
# Note: Below TRUE needs to be in R style boolean
gp <- geneplexus$GenePlexus()
input_genes <- c("ARL6", "BBS1", "BBS10", "BBS12", "BBS2", "BBS4",
                 "BBS5", "BBS7", "BBS9", "CCDC28B", "CEP290", "KIF7",
                 "MKKS", "MKS1", "TRIM32", "TTC8", "WDPCP")
# Note: Below need to use $ and not . to access pacakge methods
gp$load_genes(input_genes)
gp$fit_and_predict()
write.csv(gp$df_probs,file="probs.csv")