seqSim: A seqSim function

In vasily-pavelko/recan: R package to Explore and Discover Recombination Events in Viral Genomes

A seqSim function

Description

recan is a R package which allows to construct genetic distance plots to explore and discover recombination events in viral genomes. This method has been previously implemented in desktop software tools: RAT, Simplot and RDP4. Single function calculates sequence similarity along the alignment in a narrow window with customized step and save in dataframe. This dataframe can be used for plots and further analysis.

Usage

seqSim(seq, ref = 1, shift = 50, window = 200, region = c(0, 0))

Arguments

seq	as input we use fasta object from bio3d package. It is a multiple alignment of three or more sequences.
ref	is a sequence which is used for sequences similarity calculation.
shift	the step our window slides downstream the alignment. It's value is set to 200 by default
window	sliding window size. The number of nucleotides the sliding window will span. It has the value of 50 by default.
region	we can slice the alignment by using this parameter. region must be a a vector with two integers: the start and the end position of the alignment slice. A sequence similarity plot will be built for specified region.

Examples

seqSim(seq, ref = 2, shift = 100, window = 100, region = c(100, 3000))
seqSim_data

vasily-pavelko/recan documentation built on April 13, 2022, 1:20 p.m.