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onemap (version 2.8.2)

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

686

Version

2.8.2

License

GPL-3

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Repository

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

Maintainer

Cristiane Taniguti

Last Published

February 11th, 2022

Functions in onemap (2.8.2)

Combine OneMap datasets

Bonferroni_alpha

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

Creates a new sequence by adding markers.

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

Dataset needed for build Outcrossing vignette. It is the result from compare function exemplified there.

Add the redundant markers removed by create_data_bins function

Creates a new sequence by dropping markers.

Onemap object sanity check

create_data_bins

New dataset based on bins

empty_onemap_obj

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

Extract allele counts of progeny and parents of vcf file

filter_2pts_gaps

Filter markers based on 2pts distance

Twopts object sanity check

Draw a genetic map

Apply Kosambi mapping function

Assign markers to linkage groups

Filter markers according with a missing data threshold

Construct the linkage map for a sequence of markers

Create a sequence of markers based on other OneMap object types

Draw a linkage map

est_map_hmm_out

C++ routine for multipoint analysis in outcrossing populations

plot.onemap_progeny_haplotypes

Plots progeny haplotypes

plot.onemap_progeny_haplotypes_counts

Plot recombination breakpoints counts for each individual

create_depths_profile

Create database and ggplot graphic of allele reads depths

Show the results of grouping procedure

Print method for object class 'sequence'

print method for object class 'compare'

Print method for object class 'rf_2pts'

parents_haplotypes

Generates data.frame with parents estimated haplotypes

Function filter genotypes by genotype probability

Build genotype probabilities matrix for hmm

onemap_example_f2

Simulated data from a F2 population

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

onemap_example_out

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

Apply Haldane mapping function

print.onemap_bin

print method for object class 'onemap_bin'

Print method for object class 'onemap'

Read data from a Mapmaker raw file

Assign markers to linkage groups

Compares and displays plausible alternative orders for a given linkage group

Assign markers to preexisting linkage groups

OneMap interface with MDSMap package with possibilitie of multipoint distances estimation

Allocate markers into bins

mapmaker_example_f2

Simulated data from a F2 population

Read data from all types of progenies supported by OneMap

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

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_by_segreg_type

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

onemap_example_bc

Simulated data from a backcross population

Informs the segregation patterns of markers

plot.group.upgma

Show the results of grouping procedure

A parallelized version of map function

Show markers with/without segregation distortion

test_segregation_of_a_marker

test_segregation_of_a_marker

Extract marker number by name

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

Remove duplicated markers keeping the one with less missing data

generate_overlapping_batches

Function to divide the sequence in batches with user defined size

map_avoid_unlinked

Repeat HMM if map find unlinked marker

onemap_read_vcfR

Convert vcf file to onemap object

print.onemap_segreg_test

Show the results of segregation tests

onemap_example_riself

Simulated data from a RIL population produced by selfing.

Print order_seq object

Remove individuals from the onemap object

Defines the default mapping function

Recombination Counting and Ordering

map_overlapping_batches

Mapping overlapping batches

Sort markers in onemap object by their position in reference genome

Split rf_2pts object by markers

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.

Suggests a LOD Score for two point tests

vcf_example_out

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

test_segregation

test_segregation

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

Print method for object class 'try'

Split onemap data sets

These functions are defunct and no longer available.

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

Write a genetic map to a file

Two-point analysis between genetic markers

progeny_haplotypes

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

Plots pairwise recombination fractions and LOD Scores in a heatmap

Unidirectional Growth

Run try_seq considering previous sequence

progeny_haplotypes_counts

Plot number of breakpoints by individuals

pick_batch_sizes

Picking optimal batch size values

print.group_seq

Show the results of grouping markers to preexisting sequence

print.group.upgma

Show the results of grouping procedure

write_onemap_raw

Convert onemap object to onemap raw file

Rapid Chain Delineation