# Construction of Genetic Maps in Experimental Crosses

## Documentation for package ‘onemap’ version 3.2.1

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

## Help Pages

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
Bonferroni_alpha | Calculates individual significance level to be used to achieve a global alpha (with Bonferroni)
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_dataframe_for_plot_outcross | Create a dataframe suitable for a ggplot2 graphic
create_data_bins | New dataset based on bins
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
mapmaker_example_f2 | Simulated data from a F2 population
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.
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
order_seq | Search for the best order of markers combining compare and try_seq functions
ord_by_geno | Order the markers in a sequence using the genomic position
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