q.sort {QuESTr}

Sort and truncate genes according to the strength of gene-environment interaction

Description

Sort and truncate genes according to the strength of gene-environment interaction

Usage

q.sort(x, y, method = "linear", n.gene = ncol(x), trunc = 1)

Arguments

x

A data matrix (raw: samples, col: genes).

y

A vector of an environment in which the samples were collected.

method

A string to specify the method of regression for calculating R-squared values. "linear" (default), "quadratic" or "cubic" regression model can be specified.

n.gene

The number of genes to be included in QuEST model (default: ncol(x)).

trunc

a threshold to be truncated (default: 1).

Value

A data matrix (raw: samples, col: sorted genes)

Author(s)

Takahiko Koizumi

Examples

data(Pinus)
train <- q.clean(Pinus$train)
target <- Pinus$target
cor(target, train[, 1])

train <- q.sort(train, target, trunc = 0.5)
cor(target, train[, 1])