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


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Documentation for package ‘onemap’ version 2.1.3

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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