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onemap (version 3.2.0)

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

642

Version

3.2.0

License

GPL-3

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Repository

https://github.com/cristianetaniguti/onemap

Maintainer

Cristiane Taniguti

Last Published

January 10th, 2025

Functions in onemap (3.2.0)

Creates a new sequence by adding markers.

export_viewpoly

Export OneMap maps to be visualized in VIEWpoly

Add the redundant markers removed by create_data_bins function

Onemap object sanity check

Twopts object sanity check

create_data_bins

New dataset based on bins

Bonferroni_alpha

Calculates individual significance level to be used to achieve a global alpha (with Bonferroni)

Perform gaussian sum

edit_order_onemap

Edit sequence ordered by reference genome positions comparing to another set order

Creates a new sequence by dropping markers.

Filter markers according with a missing data threshold

Function filter genotypes by genotype probability

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

Extract allele counts of progeny and parents of vcf file

Build genotype probabilities matrix for hmm

Assign markers to preexisting linkage groups

Construct the linkage map for a sequence of markers

Assign markers to linkage groups

Apply Haldane mapping function

filter_2pts_gaps

Filter markers based on 2pts distance

Assign markers to linkage groups

keep_only_selected_mks

Keep in the onemap and twopts object only markers in the sequences

map_avoid_unlinked

Repeat HMM if map find unlinked marker

Apply Kosambi mapping function

onemap_example_f2

Simulated data from a F2 population

onemap_example_out

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

Order the markers in a sequence using the genomic position

mapmaker_example_f2

Simulated data from a F2 population

Informs the segregation patterns of markers

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

Show the results of grouping procedure

plot_genome_vs_cm

Draws a physical vs cM map

print method for object class 'compare'

print.group_seq

Show the results of grouping markers to preexisting sequence

print.group.upgma

Show the results of grouping procedure

OneMap interface with MDSMap package with option for multipoint distances estimation

Print method for object class 'onemap'

onemap_example_bc

Simulated data from a backcross population

Print method for object class 'sequence'

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.

Print method for object class 'try'

empty_onemap_obj

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

print.onemap_bin

print method for object class 'onemap_bin'

Combine OneMap datasets

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

Read data from all types of progenies supported by OneMap

print.onemap_segreg_test

Show the results of segregation tests

Show markers with/without segregation distortion

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.

Defines the default mapping function

Recombination Counting and Ordering

plot.group.upgma

Show the results of grouping procedure

map_overlapping_batches

Mapping overlapping batches

est_map_hmm_out

C++ routine for multipoint analysis in outcrossing populations

onemap_example_riself

Simulated data from a RIL population produced by selfing.

Draw a genetic map

Draw a linkage map

simu_example_f2

Simulated data from a f2 intercross population

Suggests a LOD Score for two point tests

load_onemap_sequences

Load list of sequences saved by save_onemap_sequences

generate_overlapping_batches

Function to divide the sequence in batches with user defined size

simu_example_bc

Simulated data from a backcross population

Create a sequence of markers based on other OneMap object types

parents_haplotypes

Generates data.frame with parents estimated haplotypes

Extract marker number by name

Split rf_2pts object by markers

Split onemap data sets

vcf_example_out

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

Draw a graphic of raw data for any OneMap population

Allocate markers into bins

plot.onemap_progeny_haplotypes_counts

Plot recombination breakpoints counts for each individual

plot.onemap_progeny_haplotypes

Plots progeny haplotypes

onemap_read_vcfR

Convert vcf file to onemap object

pick_batch_sizes

Picking optimal batch size values

Remove individuals from the onemap object

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 order_seq object

Two-point analysis between genetic markers

summary_maps_onemap

Create table with summary information about the linkage map

Print method for object class 'rf_2pts'

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

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

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

vcf_example_riself

Data generated from VCF file with biallelic markers from a RIL population produced by selfing

Compares and displays plausible alternative orders for a given linkage group

progeny_haplotypes

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

Run try_seq considering previous sequence

Remove duplicated markers keeping the one with less missing data

save_onemap_sequences

Save a list of onemap sequence objects

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

These functions are defunct and no longer available.

Unidirectional Growth

progeny_haplotypes_counts

Plot number of breakpoints by individuals

write_onemap_raw

Convert onemap object to onemap raw file

Write a genetic map to a file

Read data from a Mapmaker raw file

Sort markers in onemap object by their position in reference genome

test_segregation

test_segregation

test_segregation_of_a_marker

test_segregation_of_a_marker

Rapid Chain Delineation

simu_example_out

Simulated data from a outcrossing population

export_mappoly_genoprob

Export genotype probabilities in MAPpoly format (input for QTLpoly)