SimRAD: Simulations to Predict the Number of RAD and GBS Loci

Provides a number of functions to simulate restriction enzyme digestion, library construction and fragments size selection to predict the number of loci expected from most of the Restriction site Associated DNA (RAD) and Genotyping By Sequencing (GBS) approaches. SimRAD estimates the number of loci expected from a particular genome depending on the protocol type and parameters allowing to assess feasibility, multiplexing capacity and the amount of sequencing required.

Author
Olivier Lepais [aut, cre], Jason Weir [aut]
Date of publication
2016-01-06 17:22:25
Maintainer
Olivier Lepais <olepais@st-pee.inra.fr>
License
GPL-2
Version
0.96

View on CRAN

Man pages

adapt.select
Function to select fragments according to the flanking...
exclude.seqsite
Function to exclude fragments containing a specified...
insilico.digest
Function to digest DNA sequence using one or two restriction...
insilico.digest.internal
Internal function to digest DNA sequence using one...
ref.DNAseq
Function to import a reference DNA sequence from a Fasta...
sim.DNAseq
Function to simulate randomly generated DNA sequence.
SimRAD-package
Simulations to predict the number of loci expected in RAD and...
size.select
Function to select fragments according to their size.

Files in this package

SimRAD
SimRAD/NAMESPACE
SimRAD/R
SimRAD/R/ref.DNAseq.R
SimRAD/R/insilico.digest.R
SimRAD/R/adapt.select.R
SimRAD/R/exclude.seqsite.R
SimRAD/R/size.select.R
SimRAD/R/insilico.digest.internal.R
SimRAD/R/sim.DNAseq.R
SimRAD/MD5
SimRAD/DESCRIPTION
SimRAD/man
SimRAD/man/insilico.digest.Rd
SimRAD/man/adapt.select.Rd
SimRAD/man/sim.DNAseq.Rd
SimRAD/man/exclude.seqsite.Rd
SimRAD/man/ref.DNAseq.Rd
SimRAD/man/SimRAD-package.Rd
SimRAD/man/size.select.Rd
SimRAD/man/insilico.digest.internal.Rd