quest: Construct and apply the QuEST model with your own data

In takakoizumi/QuEST: Constructing Quantitative Environment Sensor using Transcriptomes

Description

Construct and apply the QuEST model with your own data

Usage

quest(x, y, newx = x, method = "linear", lower.thr = 0, n.gene = 0)

Arguments

x	A data matrix (row: samples, col: genes).
y	A vector of an environment in which the samples were collected.
newx	A data matrix. Columns of newx and x must be identical (row: samples, col: genes).
method	A string to specify the method of regression for calculating R-squared values. "linear" (default), "quadratic" or "cubic" regression model can be specified.
lower.thr	The lower threshold of R-squared value to be used in QuEST model (default: 0).
n.gene	The number of candidate genes to be used in QuEST model (default: 30).

Value

A vector of the environment in which the samples of newx were collected

Author(s)

Takahiko Koizumi

Examples

data(Pinus)
train <- q.clean(Pinus$train)
test <- Pinus$test
test <- test[, colnames(train)]
target <- Pinus$target

result <- quest(train, target, newx = test, method = "cubic")
cor(result, target)

takakoizumi/QuEST documentation built on Dec. 31, 2021, 12:06 a.m.