In ksamuk/syntR: Detection of synteny blocks via comparison of genetics maps

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)

syntR

syntR is an R package for the reproducible identification of synteny blocks and chromosomal rearrangments via comparison of two genetic maps. syntR implements an error-aware clustering algorithm specifically designed for the highly linear structure of comparative genetic map data. syntR can be used to identify synteny blocks using any type of ordered genetic markers.

Github Repository

https://github.com/ksamuk/syntR

Installation

You can install syntR from Github with:

install.packages("devtools")
devtools::install_github("ksamuk/syntR")

Example

Find synteny blocks shared between Helianthus petiolaris and Helianthus annus (provided as example data):

# load the syntR library
library("syntR")

# load data
data(ann_pet_map)

# convert data to a single ordered scale
map_list <- make_one_map(ann_pet_map)

# find synteny blocks
synt_blocks <- find_synteny_blocks(map_list, max_clust_range = 2, max_nn_dist = 10, plots = TRUE)

# print the resulting synteny blocks dataframe
synt_blocks[[2]]

Authors

Katherine Ostevik and Kieran Samuk.

See Also

GRIMM - A tool for analyzing rearrangements in pairs of genomes, including unichromosomal and multichromosomal genomes, and signed and unsigned data.

Flagel et al. 2018 - An example of a more formal model-based approach to a similar problem.

ksamuk/syntR documentation built on Feb. 11, 2021, 4:46 a.m.