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onemap (version 2.1.1)

Construction of Genetic Maps in Experimental Crosses: Full-Sib, RILs, F2 and Backcrosses

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

2.1.1

License

GPL-3

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Repository

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

Maintainer

Cristiane Taniguti

Last Published

October 18th, 2017

Functions in onemap (2.1.1)

Combine OneMap datasets

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

Draw a genetic map

Creates a new sequence by dropping markers.

est_map_hmm_out

C++ routine for multipoint analysis in outcrossing populations

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

Bonferroni_alpha

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

Creates a new sequence by adding markers.

create_data_bins

New dataset based on bins

create_dataframe_for_plot_outcross

Create a dataframe suitable for a ggplot2 graphic

Construct the linkage map for a sequence of markers

Mapping functions Haldane and Kosambi

onemap_example_f2

Simulated data from a F2 population

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

mapmaker_example_bc

Simulated data from a backcross population

mapmaker_example_f2

Simulated data from a F2 population

plot_by_segreg_type

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

Create a sequence of markers

Draw a graphic of raw data for any OneMap population

plot.onemap_segreg_test

Plot p-values for chi-square tests of expected segregation

Allocate markers into bins

Assign markers to linkage groups

print.group_seq

Show the results of grouping markers to preexisting sequence

print.onemap_segreg_test

Show the results of segregation tests

Assign markers to preexisting linkage groups

Defines the default mapping function

Suggests a LOD Score for two point tests

test_segregation

test_segregation

Read data from all types of progenies supported by OneMap

Recombination Counting and Ordering

Write a genetic map to a file

Informs the segregation patterns of markers

onemap-internal

Internal onemap functions

Print method for object class 'rf_2pts'

Two-point analysis between genetic markers

Plots pairwise recombination fractions and LOD Scores in a heatmap

test_segregation_of_a_marker

test_segregation_of_a_marker

Show the results of grouping procedure

Compares and displays plausible alternative orders for a given linkage group

Show markers with/without segregation distortion

Unidirectional Growth

Convert variants from a VCF file to OneMap file format

Print method for object class 'try'

Rapid Chain Delineation

Read data from a Mapmaker raw file

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 intercross population

vcf_example_out

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