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

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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.

Author
Gabriel Margarido [aut], Marcelo Mollinari [aut, cre], Karl Broman [ctb], Augusto Garcia [ctb]
Date of publication
2013-09-09 20:03:53
Maintainer
Marcelo Mollinari <mmollina@usp.br>
License
GPL-3
Version
2.0-4

View on CRAN

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

Files in this package

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