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 |