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onemap (version 3.0.0)

Construction of Genetic Maps in Experimental Crosses

Description

Analysis of molecular marker data from model (backcrosses, F2 and recombinant inbred lines) and non-model systems (i. e. outcrossing species). For the later, it allows statistical analysis by simultaneously estimating linkage and linkage phases (genetic map construction) according to Wu et al. (2002) . All analysis are based on multipoint approaches using hidden Markov models.

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Install

install.packages('onemap')

Monthly Downloads

590

Version

3.0.0

License

GPL-3

Issues

0

Pull Requests

1

Stars

36

Forks

23

Maintainer

Cristiane Taniguti

Last Published

November 26th, 2022

Functions in onemap (3.0.0)

create_depths_profile

Create database and ggplot graphic of allele reads depths
est_map_hmm_out

C++ routine for multipoint analysis in outcrossing populations
drop_marker

Creates a new sequence by dropping markers.
create_probs

Build genotype probabilities matrix for hmm
filter_missing

Filter markers according with a missing data threshold
extract_depth

Extract allele counts of progeny and parents of vcf file
filter_2pts_gaps

Filter markers based on 2pts distance
empty_onemap_obj

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

Draw a genetic map
draw_map2

Draw a linkage map
group_upgma

Assign markers to linkage groups
generate_overlapping_batches

Function to divide the sequence in batches with user defined size
group

Assign markers to linkage groups
filter_prob

Function filter genotypes by genotype probability
find_bins

Allocate markers into bins
haldane

Apply Haldane mapping function
group_seq

Assign markers to preexisting linkage groups
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
onemap_example_f2

Simulated data from a F2 population
onemap_example_out

Data from a full-sib family derived from two outbred parents
map_avoid_unlinked

Repeat HMM if map find unlinked marker
map

Construct the linkage map for a sequence of markers
marker_type

Informs the segregation patterns of markers
mapmaker_example_f2

Simulated data from a F2 population
order_seq

Search for the best order of markers combining compare and try_seq functions
parents_haplotypes

Generates data.frame with parents estimated haplotypes
mds_onemap

OneMap interface with MDSMap package with option for multipoint distances estimation
plot.onemap_progeny_haplotypes_counts

Plot recombination breakpoints counts for each individual
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.onemap_progeny_haplotypes

Plots progeny haplotypes
onemap_example_bc

Simulated data from a backcross population
print.group.upgma

Show the results of grouping procedure
print.group

Show the results of grouping procedure
print.order

Print order_seq object
print.group_seq

Show the results of grouping markers to preexisting sequence
print.onemap

Print method for object class 'onemap'
print.rf_2pts

Print method for object class 'rf_2pts'
progeny_haplotypes

Generate data.frame with genotypes estimated by HMM and its probabilities
progeny_haplotypes_counts

Plot number of breakpoints by individuals
onemap_example_riself

Simulated data from a RIL population produced by selfing.
onemap_read_vcfR

Convert vcf file to onemap object
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.
print.onemap_bin

print method for object class 'onemap_bin'
print.onemap_segreg_test

Show the results of segregation tests
map_overlapping_batches

Mapping overlapping batches
print.compare

print method for object class 'compare'
print.sequence

Print method for object class 'sequence'
plot_by_segreg_type

Draw a graphic showing the number of markers of each segregation pattern.
pick_batch_sizes

Picking optimal batch size values
plot.group.upgma

Show the results of grouping procedure
print.try

Print method for object class 'try'
record

Recombination Counting and Ordering
seeded_map

Construct the linkage map for a sequence of markers after seeding phases
read_onemap

Read data from all types of progenies supported by OneMap
select_segreg

Show markers with/without segregation distortion
rcd

Rapid Chain Delineation
seq_by_type

Extract marker number by name
read_mapmaker

Read data from a Mapmaker raw file
set_map_fun

Defines the default mapping function
ripple_seq

Compares and displays plausible alternative orders for a given linkage group
vcf_example_bc

Data generated from VCF file with biallelic markers from a f2 backcross population
vcf2raw

These functions are defunct and no longer available.
try_seq

Try to map a marker into every possible position between markers in a given map
test_segregation_of_a_marker

test_segregation_of_a_marker
split_2pts

Split rf_2pts object by markers
rm_dupli_mks

Remove duplicated markers keeping the one with less missing data
sort_by_pos

Sort markers in onemap object by their position in reference genome
split_onemap

Split onemap data sets
vcf_example_f2

Data generated from VCF file with biallelic markers from a f2 intercross population
seriation

Seriation
try_seq_by_seq

Run try_seq considering previous sequence
remove_inds

Remove individuals from the onemap object
rf_snp_filter_onemap

Filter markers according with a two-points recombination fraction and LOD threshold. Adapted from MAPpoly.
rf_2pts

Two-point analysis between genetic markers
vcf_example_out

Data generated from VCF file with biallelic markers from a full-sib family derived from two outbred parents
ug

Unidirectional Growth
rf_graph_table

Plots pairwise recombination fractions and LOD Scores in a heatmap
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
suggest_lod

Suggests a LOD Score for two point tests
test_segregation

test_segregation
write_onemap_raw

Convert onemap object to onemap raw file
create_dataframe_for_plot_outcross

Create a dataframe suitable for a ggplot2 graphic
compare

Compare all possible orders (exhaustive search) for a given sequence of markers
combine_onemap

Combine OneMap datasets
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.
create_data_bins

New dataset based on bins
add_redundants

Add the redundant markers removed by create_data_bins function
check_data

Onemap object sanity check
check_twopts

Twopts object sanity check