# Software for the Creation of High Density Linkage Maps in Outcrossing Species

## Documentation for package ‘BatchMap’ version 1.0.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

add.marker | Creates a new sequence by adding markers.
Bonferroni.alpha | Calculates individual significance level to be used to achieve a global alpha (with Bonferroni)
combine.onemap | Combine OneMap datasets
compare | Compare all possible orders (exhaustive search) for a given sequence of markers
create.data.bins | New dataset based on bins
create.dataframe.for.plot.outcross | Create a dataframe suitable for a ggplot2 graphic
draw.map | Draw a genetic map
drop.marker | Creates a new sequence by dropping markers.
example.out | Data from a full-sib family derived from two outbred parents
find.bins | Allocate markers into bins
group | Assign markers to linkage groups
haldane | Mapping functions Haldane and Kosambi
kosambi | Mapping functions Haldane and Kosambi
make.seq | Create a sequence of markers
map | Construct the linkage map for a sequence of markers
map.overlapping.batches | Mapping overlapping batches
map_func | Mapping functions Haldane and Kosambi
marker.type | Informs the segregation patterns of markers
order.seq | Search for the best order of markers combining compare and try.seq functions
pick.batch.sizes | Picking optimal batch size values
plot.by.segreg.type | Draw a graphic showing the number of markers of each segregation pattern.
plot.onemap | Draw a graphic of raw data for any OneMap population
plot.onemap.segreg.test | Plot p-values for chi-square tests of expected segregation
print.group | Print group result
print.onemap.segreg.test | Print segregation test result
print.outcross | Print read.outcross result
print.rf.2pts | Print twopoint test result
print.try | Print try.seq result
pseudo.testcross.split | Split a dataset into parent-specific subsets
rcd | Rapid Chain Delineation
read.mapmaker | Read data from a Mapmaker raw file
read.onemap | Read data from all types of progenies supported by OneMap
read.outcross | Read data from a full-sib progeny (outcrossing populations)
read.outcross2 | Read data from a full-sib progeny (outcrossing populations)
record | Recombination Counting and Ordering
record.parallel | Recombination Counting and Ordering
rf.2pts | Two-point analysis between genetic markers
ripple.ord | Update linkage map with alternative orders at all positions
ripple.seq | Compares and displays plausible alternative orders for a given linkage group
ripple.window | Update linkage map with alternative orders at a given position
seeded.map | Construct the linkage map for a sequence of markers after seeding phases
select.segreg | Show markers with/without segregation distortion
seriation | Seriation
set.map.fun | Defines the default mapping function
suggest.lod | Suggests a LOD Score for two point tests
test.segregation | test.segregation
test.segregation.of.a.marker | test.segregation.of.a.marker
try.seq | Try to map a marker into every possible position between markers in a given map
ug | Unidirectional Growth
write.map | Write a genetic map to a file