q.opt: Estimate the optimal number of genes to construct QuEST model

In QuESTr: Constructing Quantitative Environment Sensor using Transcriptomes

Estimate the optimal number of genes to construct QuEST model

Description

Estimate the optimal number of genes to construct QuEST model

Usage

q.opt(x, y, range = 5:50, method = "linear", rep = 1)

Arguments

x	A data matrix (row: samples, col: genes).
y	A vector of an environment in which the samples were collected.
range	A sequence of numbers of genes to be tested for MAE calculation (default: 5:50).
method	A string to specify the method of regression for calculating R-squared values. "linear" (default), "quadratic" or "cubic" regression model can be specified.
rep	The number of replications for each case set by range (default: 1).

Value

A sample-MAE curve

Author(s)

Takahiko Koizumi

Examples

data(Pinus)
train <- q.clean(Pinus$train)
target <- Pinus$target
q.opt(train[1:10, ], target[1:10], range = 5:15)

QuESTr documentation built on March 18, 2022, 5:09 p.m.