A method for prediction of environmental conditions based on transcriptome data linked with the environmental gradients. This package provides functions to overview gene-environment relationships, to construct the prediction model, and to predict environmental conditions where the transcriptomes were generated. This package can quest for candidate genes for the model construction even in non-model organisms' transcriptomes without any genetic information.
The goal of QuESTr is to provide the functions to construct a prediction model of environments using transcriptomes linked with the environments based on QuEST algorithm. This package can quest for candidate genes for the model construction even in non-model organinsms’ transcriptomes without any genetic information.
You can install the development version of QuESTr from
GitHub with:
#install.packages(“devtools”)
devtools::install_github(“takakoizumi/QuESTr”)
install.packages(“QuESTr”)
library(QuESTr)
# basic example code
data(Pinus)
x.train <- Pinus[[1]]
x.test <- Pinus[[2]]
y <- Pinus[[3]]
cor(y, quest(x.train, y, newx = x.test, n.gene = 100))