q.sort: Sort and truncate genes according to the strength of...

In takakoizumi/QuEST: Constructing Quantitative Environment Sensor using Transcriptomes

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])
ncol(train)

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

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