In arendsee/synder: Use Synteny to Filter Genomic Search

Other vignettes:

• introduction to Synder
• algorithmic details
• a case study in yeast

The primary function of synder is to map genomic intervals of interest from a query genome to search intervals in the target genome. In this vignette, I will showcase the basic functionallity using a toy data set.

For algorithmic details see this vignette.

This work is funded by the National Science Foundation grant NSF-IOS 1546858.

Installation

Synder is available from github, installation requires devtools:

devtools::install_github('arendsee/synder')

# imports required for this vignette
library(synder)
library(knitr)
library(magrittr)
library(ggplot2)
library(dplyr)
library(readr)

Mapping intervals on the simple linear synteny map

Sample raw data, as data.frames rather than the dedicated Bioconductor types, can be found in intro_1, intro_2 and toy.

data(intro_1)

This dataset contains the following synteny map, which can be converted to a data.frame with as.data.frame.

knitr::kable(as.data.frame(intro_1$synmap))

(syn <- intro_1$synmap)

The synmap object has specialized print and plot functions.

class(syn)

The print function is curtesy of the inherited GRangePairs class

print(syn)

The plot function shows the synteny map as an alignment.

plot(syn)

We can map intervals from query to target interactively with the anon_search function.

x <- anon_search(syn, 240, 260, 'que')
plot(x, syn)

The plot function here takes the search results and plots them in the context of the synteny map. The x-axis shows position relative to the query, and the y-axis relative to the target. The anon_search and search functions map between th axes.

Notice that the search interval snaps to the size of the gap in the target synteny map.

x <- anon_search(syn, 240, 310, 'que')
plot(x, syn)

Both sides snap to the nearest target edge.

Inversions and contiguous sets

synder breaks synteny maps into contiguous sets of syntenic intervals. The sets are defined as sequences of syntenic intervals that are adjacent on both the query and target side and are not overlapping.

data(intro_2)
plot(intro_2$synmap)
plot(synder::dump(intro_2$synmap))

arendsee/synder documentation built on May 10, 2019, 1:26 p.m.