xoi: Tools for Analyzing Crossover Interference

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

Author
Karl W Broman <kbroman@biostat.wisc.edu>, with contributions from Il-Youp Kwak
Date of publication
2015-10-18 17:20:01
Maintainer
Karl W Broman <kbroman@biostat.wisc.edu>
License
GPL-3
Version
0.66-9
URLs

View on CRAN

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

Files in this package

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