intens_theta: Preprocess raw values and calculate Intensity and Theta...
In gsrc: Genome Structure Rearrangement Calling in Genomes with High Synteny

Preprocess raw values and calculate Intensity and Theta values

1 2	intens_theta(raw, norm = "quantile", scaling = "mean", transf = "log", pn = 2)

`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.

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

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

dat <- intens_theta(raw_napus)
}

gsrc documentation built on May 30, 2017, 4:16 a.m.

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