onemap: Software for constructing genetic maps in experimental crosses: full-sib, RILs, F2 and backcrosses
Version 2.0-4

Analysis of molecular marker data from model (backcrosses, F2 and recombinant inbred lines) and non-model systems (i. e. outcrossing species). For the later, it allows statistical analysis by simultaneously estimating linkage and linkage phases (genetic map construction). All analysis are based on multipoint approaches using hidden Markov models.

AuthorGabriel Margarido [aut], Marcelo Mollinari [aut, cre], Karl Broman [ctb], Augusto Garcia [ctb]
Date of publication2013-09-09 20:03:53
MaintainerMarcelo Mollinari <mmollina@usp.br>
LicenseGPL-3
Version2.0-4
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("onemap")

Getting started

Package overview

Popular man pages

add_drop: Add or Drop Markers From a Sequence
group: Assign markers to linkage groups
make.seq: Create a sequence of markers
map: Construct the linkage map for a sequence of markers
map_func: Mapping functions Haldane and Kosambi
marker.type: Informs the segregation patterns of markers
onemap-package: Software for constructing genetic maps
See all...

All man pages Function index File listing

Man pages

add_drop: Add or Drop Markers From a Sequence
compare: Compare all possible orders (exhaustive search) for a given...
def.rf.3pts: Three-point analysis of genetic markers
draw.map: Draw a genetic map
example.out: Data from a full-sib family derived from two outbred parents
fake.bc.onemap: Simulated data from a backcross population
fake.f2.onemap: Simulated data from a F2 population
group: Assign markers to linkage groups
make.seq: Create a sequence of markers
map: Construct the linkage map for a sequence of markers
map_func: Mapping functions Haldane and Kosambi
marker.type: Informs the segregation patterns of markers
onemap-internal: Internal onemap functions
onemap-package: Software for constructing genetic maps
order.seq: Search for the best order of markers combining compare and...
rcd: Rapid Chain Delineation
read.mapmaker: Read data from a Mapmaker raw file
read.outcross: Read data from a segregating full-sib population
record: Recombination Counting and Ordering
rf.2pts: Two-point analysis between genetic markers
rf.graph.table: Plots pairwise recombination fractions and LOD Scores using a...
ripple.seq: Compares and displays plausible alternative orders for a...
seriation: Seriation
set.map.fun: Defines the default mapping function
try.seq: Try to map a marker into every possible position between...
ug: Unidirectional Growth
write.map: Write a genetic map to a file

Functions

Cindex Man page Source code
acum Man page Source code
add.marker Man page Source code
add_drop Man page
adjust.rf.ril Man page Source code
avoid.reverse Man page Source code
codif.data Man page Source code
comb Man page Source code
comb.ger Man page Source code
compare Man page Source code
cr2pts Man page Source code
cr3pts Man page Source code
def.rf.3pts Man page Source code
diplo Man page Source code
draw.map Man page Source code
draw.order Man page Source code
draw.rf.inter Man page Source code
draw.try Man page Source code
drop.marker Man page Source code
est.map.c Man page Source code
example.out Man page
fake.bc.onemap Man page
fake.f2.onemap Man page
group Man page Source code
haldane Man page Source code
kosambi Man page Source code
make.seq Man page Source code
map Man page Source code
map_func Man page
marker.type Man page Source code
onemap Man page
onemap-package Man page
order.seq Man page Source code
perm.pars Man page Source code
perm.tot Man page Source code
phases Man page Source code
plotFunction.out Man page Source code
print.bc.onemap Man page Source code
print.compare Man page Source code
print.f2.onemap Man page Source code
print.group Man page Source code
print.order Man page Source code
print.outcross Man page Source code
print.rf.2pts Man page Source code
print.rf.3pts Man page Source code
print.riself.onemap Man page Source code
print.risib.onemap Man page Source code
print.sequence Man page Source code
print.try Man page Source code
rcd Man page Source code
read.mapmaker Man page Source code
read.outcross Man page Source code
record Man page Source code
rem.amb.ph Man page Source code
return.geno Man page Source code
rf.2pts Man page Source code
rf.graph.table Man page Source code
ripple.seq Man page Source code
ser.ord Man page Source code
seriation Man page Source code
set.map.fun Man page Source code
try.seq Man page Source code
ug Man page Source code
write.map Man page Source code

Files

inst
inst/BUGS
inst/CITATION
inst/HISTORY
inst/example
inst/example/example.out.txt
inst/example/fake.bc.onemap.raw
inst/example/fake.f2.onemap.raw
inst/doc
inst/doc/Tutorial_Onemap_reduced_version.Rnw
inst/doc/Tutorial_Onemap_reduced_version.pdf
inst/doc/Tutorial_Onemap_reduced_version.R
src
src/hmm_out.h
src/twopts.c
src/threepts.h
src/hmm_out.c
src/twopts.h
src/Makevars.win
src/threepts.c
NAMESPACE
data
data/fake.bc.onemap.RData
data/example.out.RData
data/fake.f2.onemap.RData
R
R/read.outcross.R
R/make.seq.R
R/rf.2pts.R
R/phases.R
R/cr2pts.R
R/avoid.reverse.R
R/ripple.seq.R
R/ug.R
R/marker.type.R
R/read.mapmaker.R
R/drop.marker.R
R/map.R
R/adjust.rils.R
R/rcd.R
R/order.seq.R
R/map_func.R
R/try.seq.R
R/defunct.R
R/rf.graph.table.R
R/comb.ger.R
R/add.marker.R
R/seriation.R
R/group.R
R/permutations.R
R/est.map.c.R
R/compare.R
R/write.map.R
R/return.geno.R
R/codif.data.R
R/zzz.R
R/record.R
R/draw.map.R
R/acum.R
vignettes
vignettes/figures
vignettes/figures/tutorial.pdf
vignettes/figures/rconsole.png
vignettes/Tutorial_Onemap_reduced_version.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
LICENSE.note
man
man/try.seq.Rd
man/read.mapmaker.Rd
man/onemap-package.Rd
man/add_drop.Rd
man/example.out.Rd
man/group.Rd
man/map.Rd
man/fake.f2.onemap.Rd
man/rf.graph.table.Rd
man/ug.Rd
man/onemap-internal.Rd
man/set.map.fun.Rd
man/fake.bc.onemap.Rd
man/read.outcross.Rd
man/marker.type.Rd
man/rcd.Rd
man/map_func.Rd
man/record.Rd
man/draw.map.Rd
man/compare.Rd
man/def.rf.3pts.Rd
man/seriation.Rd
man/ripple.seq.Rd
man/order.seq.Rd
man/write.map.Rd
man/make.seq.Rd
man/rf.2pts.Rd
onemap documentation built on May 19, 2017, 1:11 p.m.

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