Package: ricalc 0.56-2

ricalc: Calculations for Recombinant Inbred Lines

Calculate two- and three-locus probabilities in multiple-strain recombinant inbred lines, and simulate such lines. Broman (2005) <doi:10.1534/genetics.104.035212>.

Authors:Karl W Broman [aut, cre]

ricalc_0.56-2.tar.gz
ricalc_0.56-2.zip(r-4.7)ricalc_0.56-2.zip(r-4.6)ricalc_0.56-2.zip(r-4.5)
ricalc_0.56-2.tgz(r-4.6-any)ricalc_0.56-2.tgz(r-4.5-any)
ricalc_0.56-2.tar.gz(r-4.7-any)ricalc_0.56-2.tar.gz(r-4.6-any)
ricalc_0.56-2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
ricalc/json (API)

# Install 'ricalc' in R:

install.packages('ricalc', repos = c('https://kbroman.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/kbroman/ricalc/issues

Datasets:

fulltm - Symbolic generation-to-generation transition matrices
lookup - Look-up tables for multi-locus parental types
mouseL - Estimated genetic lengths of mouse chromosomes
mtm - Symbolic transition matrices for meiosis
threept.AI - Three-point probabilities for four-way RILs by sibling mating
threept.ANI - Three-point probabilities for four-way RILs by sibling mating
threept.XI - Three-point probabilities for four-way RILs by sibling mating
threept.XNI - Three-point probabilities for four-way RILs by sibling mating

On CRAN:

2.18 score 3 stars 38 exports 0 dependencies

Last updated from:e2915d698b. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	111
source / vignettes	OK	189
linux-release-x86_64	OK	102
macos-release-arm64	OK	78
macos-oldrel-arm64	OK	75
windows-devel	OK	70
windows-release	OK	62
windows-oldrel	OK	55
wasm-release	OK	90

Exports:adjust.order alternates coinc.gam convert.full.tm convert2gen count.absorb create.parent cross exchangeg genAILped get.full.tm get.full.tm.symbolic get.meiosis.tm get.meiosis.tm.symbolic get.ril.coinc get.ril.prob get.start gtypes imf.gam lengthHet lennum.het meiosis meiosis.sub mf.gam modifyL my.kronecker my.kronecker.symbolic nubreak read.full.tm.symbolic read.meiosis.tm.symbolic reverseg ricalcversion sim.ped sim.ri where.het write.full.tm.symbolic write.meiosis.tm.symbolic write.sparse

Dependencies:

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Overview of R/ricalc package	ricalc-package
Three-point coincidence under the gamma renewal model	coinc.gam
Convert sparse version of transition matrix to full form	convert.full.tm
Convert simulated pedigree data to genotypes at markers	convert2gen
Count absorbing states	count.absorb
Symbolic generation-to-generation transition matrices	fulltm
Generate a pedigree matrix for AIL	genAILped
Calculate the transition matrix for the formation of RILs	get.full.tm
Calculate symbolic form of transition matrix for the formation of RILs	get.full.tm.symbolic
Calculate 3-point coincidence on an RIL chromosome	get.ril.coinc
Calculate the haplotype probabilities for an RIL chromosome	get.ril.prob
Determine the initial state in the generation of RILs	get.start
Inverse map function for gamma renewal model	imf.gam
Look-up tables for multi-locus parental types	lookup
Map function for gamma renewal model	mf.gam
Estimated genetic lengths of mouse chromosomes	mouseL
Symbolic transition matrices for meiosis	mtm
Installed version of R/ricalc	ricalcversion
Simulate a general pedigree	sim.ped
Simulate a recombinant inbred line	sim.ri
Three-point probabilities for four-way RILs by sibling mating	threept.AI threept.ANI threept.XI threept.XNI