xoi: Tools for Analyzing Crossover Interference
Version 0.66-9

Analysis of crossover interference in experimental crosses, particularly regarding the gamma model.

Browse man pages Browse package API and functions Browse package files

AuthorKarl W Broman <kbroman@biostat.wisc.edu>, with contributions from Il-Youp Kwak
Date of publication2015-10-18 17:20:01
MaintainerKarl W Broman <kbroman@biostat.wisc.edu>
LicenseGPL-3
Version0.66-9
URL http://github.com/kbroman/xoi
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("xoi")

Man pages

bssbsb: BSS/BSB backcross data
chiasma: Estimate chiasma distribution from crossover counts
coincidence: Estimate coincidence function
convertxoloc: Convert format of crossover locations data
countxo: Estimate number of crossovers
distance.given.two: Distance between crossovers given there are two
est.coi: Estimate the coincidence function
est.coi.um: Estimate the coincidence as a function of micron distance
est.recrate: Estimate recombination rate
find.breaks: Estimate crossover locations
firstden: Distance to a crossover
first.given.two: Location of first crossover given there are two
fitGamma: Fit Gamma model
fitStahl: Fit Stahl model
gammacoi: Coincidence function for the gamma model
intensity: Estimate intensity function
ioden: Distance between crossovers
joint.given.two: Crossover locations given there are two
kfunc: estimate Ripley's K function
location.given.one: Location of crossover given there is one
recrate2scanone: Convert recrate to scanone format
simStahl: Simulate crossover locations under the Stahl model
stahlcoi: Coincidence function for the Stahl model
stahlLoglik: Calculate log likelihood for Stahl model
xoiversion: Installed version of R/xoi
xoprob: Distribution of number of crossovers

Functions

addlog Source code
bssbsb Man page
calc_Lstar Source code
chiasma Man page Source code
coincidence Man page Source code
coincidenceSUB Source code
convertxoloc Man page Source code
countxo Man page Source code
distance.given.two Man page Source code
est.coi Man page Source code
est.coi.um Man page Source code
est.recrate Man page Source code
find.breaks Man page Source code
find.breaks.F2 Source code
first.given.two Man page Source code
firstden Man page Source code
fitGamma Man page Source code
fitStahl Man page Source code
fitStahl.sub Source code
fitStahl.sub2 Source code
gammacoi Man page Source code
get_n_xo Source code
identify_xo Source code
inferxoloc.F2 Source code
intensity Man page Source code
intensitySUB Source code
ioden Man page Source code
joint.given.two Man page Source code
kfunc Man page Source code
location.given.one Man page Source code
recrate2scanone Man page Source code
simStahl Man page Source code
stahlLoglik Man page Source code
stahlLoglikF2 Source code
stahlcoi Man page Source code
xoiversion Man page Source code
xoprob Man page Source code

Files

inst
inst/STATUS.txt
inst/LICENSE.txt
inst/README.md
inst/INSTALL_ME.txt
tests
tests/testthat.R
tests/testthat
tests/testthat/test-est_um.R
tests/testthat/test-calc_Lstar.R
src
src/chiasma.c
src/chiasma.h
src/coi_um.c
src/GammaS.h
src/GammaUtil.c
src/coincidence.c
src/GammaDensities.c
src/kfunc.h
src/GammaS.c
src/fitStahl.c
src/recrate.c
src/coi_um.h
src/coincidence.h
src/kwak_coincidence.c
src/simStahl.c
src/kwak_intensity.c
src/GammaIntegral.c
src/stahl_util.c
src/kfunc.c
src/GammaLoglik.c
src/recrate.h
src/kwak.h
src/zeroin.c
src/stahl_util.h
src/zeroin.h
src/kwak_get_n_xo.c
src/simStahl.h
src/fitStahl.h
src/kwak_identify.c
NAMESPACE
data
data/bssbsb.RData
R
R/kwak_coincidence.R
R/fitStahl.R
R/kwak_identify_xo.R
R/gammaDensities.R
R/xoiversion.R
R/kwak_intensity.R
R/fitGamma.R
R/simStahl.R
R/coi_um.R
R/coincidence.R
R/kfunc.R
R/util.R
R/recrate.R
R/bssbsb-data.R
R/kwak_get_n_xo.R
R/chiasma.R
MD5
DESCRIPTION
man
man/stahlLoglik.Rd
man/fitGamma.Rd
man/joint.given.two.Rd
man/stahlcoi.Rd
man/chiasma.Rd
man/countxo.Rd
man/est.recrate.Rd
man/xoprob.Rd
man/distance.given.two.Rd
man/est.coi.um.Rd
man/simStahl.Rd
man/location.given.one.Rd
man/fitStahl.Rd
man/find.breaks.Rd
man/ioden.Rd
man/est.coi.Rd
man/recrate2scanone.Rd
man/kfunc.Rd
man/coincidence.Rd
man/convertxoloc.Rd
man/first.given.two.Rd
man/bssbsb.Rd
man/firstden.Rd
man/gammacoi.Rd
man/intensity.Rd
man/xoiversion.Rd
xoi documentation built on May 20, 2017, 2:10 a.m.