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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

411

Version

3.0.0

License

GPL-3

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Repository

https://github.com/augusto-garcia/onemap

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

Creates a new sequence by dropping markers.

Build genotype probabilities matrix for hmm

Filter markers according with a missing data threshold

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 a genetic map

Draw a linkage map

Assign markers to linkage groups

generate_overlapping_batches

Function to divide the sequence in batches with user defined size

Assign markers to linkage groups

Function filter genotypes by genotype probability

Allocate markers into bins

Apply Haldane mapping function

Assign markers to preexisting linkage groups

keep_only_selected_mks

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

Apply Kosambi mapping function

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

Construct the linkage map for a sequence of markers

Informs the segregation patterns of markers

mapmaker_example_f2

Simulated data from a F2 population

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

parents_haplotypes

Generates data.frame with parents estimated haplotypes

OneMap interface with MDSMap package with option for multipoint distances estimation

plot.onemap_progeny_haplotypes_counts

Plot recombination breakpoints counts for each individual

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

Show the results of grouping procedure

Print order_seq object

print.group_seq

Show the results of grouping markers to preexisting sequence

Print method for object class 'onemap'

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

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 method for object class 'compare'

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 method for object class 'try'

Recombination Counting and Ordering

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

Read data from all types of progenies supported by OneMap

Show markers with/without segregation distortion

Rapid Chain Delineation

Extract marker number by name

Read data from a Mapmaker raw file

Defines the default mapping function

Compares and displays plausible alternative orders for a given linkage group

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

These functions are defunct and no longer available.

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 rf_2pts object by markers

Remove duplicated markers keeping the one with less missing data

Sort markers in onemap object by their position in reference genome

Split onemap data sets

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

Run try_seq considering previous sequence

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.

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

Unidirectional Growth

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 a genetic map to a file

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

Combine OneMap datasets

Bonferroni_alpha

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

Perform gaussian sum

Creates a new sequence by adding markers.

create_data_bins

New dataset based on bins

Add the redundant markers removed by create_data_bins function

Onemap object sanity check

Twopts object sanity check