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onemap (version 2.0-4)

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

Description

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.

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Version

Install

install.packages('onemap')

Monthly Downloads

642

Version

2.0-4

License

GPL-3

Maintainer

Marcelo Mollinari

Last Published

September 9th, 2013

Functions in onemap (2.0-4)

set.map.fun

Defines the default mapping function
read.mapmaker

Read data from a Mapmaker raw file
ripple.seq

Compares and displays plausible alternative orders for a given linkage group
group

Assign markers to linkage groups
rcd

Rapid Chain Delineation
map

Construct the linkage map for a sequence of markers
seriation

Seriation
try.seq

Try to map a marker into every possible position between markers
read.outcross

Read data from a segregating full-sib population
rf.graph.table

Plots pairwise recombination fractions and LOD Scores using a color scale.
write.map

Write a genetic map to a file
make.seq

Create a sequence of markers
fake.f2.onemap

Simulated data from a F2 population
example.out

Data from a full-sib family derived from two outbred parents
def.rf.3pts

Three-point analysis of genetic markers
ug

Unidirectional Growth
record

Recombination Counting and Ordering
compare

Compare all possible orders (exhaustive search) for a given sequence of markers
add_drop

Add or Drop Markers From a Sequence
marker.type

Informs the segregation patterns of markers
order.seq

Search for the best order of markers combining compare and try.seq functions
onemap-internal

Internal onemap functions
map_func

Mapping functions Haldane and Kosambi
fake.bc.onemap

Simulated data from a backcross population
draw.map

Draw a genetic map
rf.2pts

Two-point analysis between genetic markers
onemap-package

Software for constructing genetic maps