Construction of Genetic Maps in Experimental Crosses

Documentation for package ‘onemap’ version 3.0.0

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.
empty_onemap_obj	Produce empty object to avoid code break. Function for internal purpose.
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
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
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.
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
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
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
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