# Construction of Genetic Maps in Experimental Crosses: Full-Sib, RILs, F2 and Backcrosses

## Documentation for package ‘onemap’ version 2.1.3

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

## 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_dataframe_for_plot_outcross | Create a dataframe suitable for a ggplot2 graphic
create_data_bins | New dataset based on bins
draw_map | Draw a genetic map
draw_map2 | Draw a linkage map
drop_marker | Creates a new sequence by dropping markers.
find_bins | Allocate markers into bins
group | Assign markers to linkage groups
group_seq | Assign markers to preexisting 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
mapmaker_example_bc | Simulated data from a backcross population
mapmaker_example_f2 | Simulated data from a F2 population
map_func | Mapping functions Haldane and Kosambi
marker_type | Informs the segregation patterns of markers
mds_onemap | OneMap interface with MDSMap package with possibilitie of multipoint distances estimation
onemap_example_bc | Simulated data from a backcross population
onemap_example_f2 | Simulated data from a F2 population
onemap_example_out | Data from a full-sib family derived from two outbred parents
onemap_example_riself | Simulated data from a RIL population produced by selfing.
onemap_read_vcfR | Convert vcfR object to onemap object
order_seq | Search for the best order of markers combining compare and try_seq functions
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
plot_by_segreg_type | Draw a graphic showing the number of markers of each segregation pattern.
print.onemap_segreg_test | Show the results of segregation tests
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
record | Recombination Counting and Ordering
rf_2pts | Two-point analysis between genetic markers
rf_graph_table | Plots pairwise recombination fractions and LOD Scores in a heatmap
ripple_seq | Compares and displays plausible alternative orders for a given linkage group
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
vcf2raw | Convert variants from a VCF file to OneMap file format
vcf_example_bc | Data generated from VCF file with biallelic markers from a f2 backcross population
vcf_example_f2 | Data generated from VCF file with biallelic markers from a f2 intercross population
vcf_example_out | Data generated from VCF file with biallelic markers from a full-sib family derived from two outbred parents
vcf_example_riself | Data generated from VCF file with biallelic markers from a RIL population produced by selfing
write_map | Write a genetic map to a file
write_onemap_raw | Convert onemap object to onemap raw file