R: HMM-Based Model for Genotyping and Cross-Over Identification

# HMM-Based Model for Genotyping and Cross-Over Identification

## Documentation for package ‘RTIGER’ version 2.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

.RTIGER | This class is a generic container for RTIGER analysis
ATseqlengths | The autosome chromosome lengths for Arabidopsis Thaliana.
calcCOnumber | Obtain number of Cross-Over events per sample and chromosome.
dev | Function to developers. It runs one EM step
fit | Call Julia code to fit the values
generateObject | Load data
myDat | A fitted example using three own samples of Arabidopsis. More information in publication:
optimize_R | Find the otimum R value for a given data set
plotCOs | Obtain number of Cross-Over events per sample and chromosome.
RTIGER | Load, Fit, and plot
RTIGER-class | This class is a generic container for RTIGER analysis
setupJulia | Installs the needed packages in JULIA to run the EM algorithm for rHMM.
sourceJulia | Function needed before using RTIGER() function. It loads the scripts in Julia that fit the rHMM.