intens_theta: Preprocess raw values and calculate Intensity and Theta...

In grafab/gsrc: Genome Structure Rearrangement Calling in Genomes with High Synteny

Description

Preprocess raw values and calculate Intensity and Theta values

Usage

intens_theta(raw, norm = "quantile", scaling = "mean", transf = "log",
  pn = 2, postnorm = FALSE)

Arguments

raw	Raw_data object.
norm	Method for the normalization. One of "none", "quantile", "median" or "both".
scaling	Logical, if each SNP should be scaled or not.
transf	Method for transformation of the raw values. "none", "log" and "fourth-root" are implemented.
pn	Numeric, p-norm for the intensity calculation.
postnorm	Logical, if intensity values should be median normalized row- and columns-wise.

Value

List with two matrices "intensity" (signal intensities) and "theta" (genotype value).

Examples

if(require(brassicaData)){
data("raw_napus", package = "brassicaData")

dat <- intens_theta(raw_napus)
}

grafab/gsrc documentation built on May 17, 2019, 8:18 a.m.