Bonferroni_alpha        Calculates individual significance level to be
                        used to achieve a global alpha (with
                        Bonferroni)
acum                    Perform gaussian sum
add_marker              Creates a new sequence by adding markers.
add_redundants          Add the redundant markers removed by
                        create_data_bins function
check_data              Onemap object sanity check
check_twopts            Twopts object sanity check
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
create_depths_profile   Create database and ggplot graphic of allele
                        reads depths
create_probs            Build genotype probabilities matrix for hmm
draw_map                Draw a genetic map
draw_map2               Draw a linkage map
drop_marker             Creates a new sequence by dropping markers.
edit_order_onemap       Edit sequence ordered by reference genome
                        positions comparing to another set order
empty_onemap_obj        Produce empty object to avoid code break.
                        Function for internal purpose.
export_mappoly_genoprob
                        Export genotype probabilities in MAPpoly format
                        (input for QTLpoly)
export_viewpoly         Export OneMap maps to be visualized in VIEWpoly
extract_depth           Extract allele counts of progeny and parents of
                        vcf file
filter_2pts_gaps        Filter markers based on 2pts distance
filter_missing          Filter markers according with a missing data
                        threshold
filter_prob             Function filter genotypes by genotype
                        probability
find_bins               Allocate markers into bins
generate_overlapping_batches
                        Function to divide the sequence in batches with
                        user defined size
group                   Assign markers to linkage groups
group_seq               Assign markers to preexisting linkage groups
group_upgma             Assign markers to linkage groups
haldane                 Apply Haldane mapping function
keep_only_selected_mks
                        Keep in the onemap and twopts object only
                        markers in the sequences
kosambi                 Apply Kosambi mapping function
load_onemap_sequences   Load list of sequences saved by
                        save_onemap_sequences
make_seq                Create a sequence of markers based on other
                        OneMap object types
map                     Construct the linkage map for a sequence of
                        markers
map_avoid_unlinked      Repeat HMM if map find unlinked marker
map_overlapping_batches
                        Mapping overlapping batches
map_save_ram            Perform map using background objects with only
                        selected markers. It saves ram memory during
                        the procedure. It is useful if dealing with
                        many markers in total data set.
mapmaker_example_f2     Simulated data from a F2 population
marker_type             Informs the segregation patterns of markers
mds_onemap              OneMap interface with MDSMap package with
                        option for 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 vcf file to onemap object
ord_by_geno             Order the markers in a sequence using the
                        genomic position
order_seq               Search for the best order of markers combining
                        compare and try_seq functions
parents_haplotypes      Generates data.frame with parents estimated
                        haplotypes
pick_batch_sizes        Picking optimal batch size values
plot.onemap             Draw a graphic of raw data for any OneMap
                        population
plot.onemap_progeny_haplotypes
                        Plots progeny haplotypes
plot.onemap_progeny_haplotypes_counts
                        Plot recombination breakpoints counts for each
                        individual
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.
plot_genome_vs_cm       Draws a physical vs cM map
print.compare           print method for object class 'compare'
print.onemap            Print method for object class 'onemap'
print.onemap_bin        print method for object class 'onemap_bin'
print.onemap_segreg_test
                        Show the results of segregation tests
print.order             Print order_seq object
print.sequence          Print method for object class 'sequence'
progeny_haplotypes      Generate data.frame with genotypes estimated by
                        HMM and its probabilities
progeny_haplotypes_counts
                        Plot number of breakpoints by individuals
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
remove_inds             Remove individuals from the onemap object
rf_2pts                 Two-point analysis between genetic markers
rf_graph_table          Plots pairwise recombination fractions and LOD
                        Scores in a heatmap
rf_snp_filter_onemap    Filter markers according with a two-points
                        recombination fraction and LOD threshold.
                        Adapted from MAPpoly.
ripple_seq              Compares and displays plausible alternative
                        orders for a given linkage group
rm_dupli_mks            Remove duplicated markers keeping the one with
                        less missing data
save_onemap_sequences   Save a list of onemap sequence objects
seeded_map              Construct the linkage map for a sequence of
                        markers after seeding phases
select_segreg           Show markers with/without segregation
                        distortion
seq_by_type             Extract marker number by name
seriation               Seriation
set_map_fun             Defines the default mapping function
simu_example_bc         Simulated data from a backcross population
simu_example_f2         Simulated data from a f2 intercross population
simu_example_out        Simulated data from a outcrossing population
sort_by_pos             Sort markers in onemap object by their position
                        in reference genome
split_2pts              Split rf_2pts object by markers
split_onemap            Split onemap data sets
suggest_lod             Suggests a LOD Score for two point tests
summary_maps_onemap     Create table with summary information about the
                        linkage map
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
try_seq_by_seq          Run try_seq considering previous sequence
ug                      Unidirectional Growth
vcf2raw                 These functions are defunct and no longer
                        available.
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
