q.rank {QuESTr}

Visualize R-squared value distribution in gene-environment interaction

Description

Visualize R-squared value distribution in gene-environment interaction

Usage

q.rank(
  x,
  y,
  method = "linear",
  lower.thr = 0,
  n.gene = ncol(x),
  upper.xlim = ncol(x)
)

Arguments

x

A data matrix (row: 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.

lower.thr

The lower threshold of R-squared value to be included in QuEST model (default: 0).

n.gene

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

upper.xlim

The upper limitation of x axis (i.e., the number of genes) in the resulted figure (default: ncol(x)).

Value

A rank order plot

Author(s)

Takahiko Koizumi

Examples

data(Pinus)
train <- q.clean(Pinus$train)
target <- Pinus$target
train <- q.sort(train, target)
q.rank(train, target)