get_syntenic_genes: get the syntenic genes as a table

In macrosyntR: Draw Ordered Oxford Grids and Chord Diagrams

get the syntenic genes as a table

Description

This is a function to extract all the syntenic genes from an orthologs_df. It requires as input an orthologs_df loaded by load_orthologs().

Usage

get_syntenic_genes(orthologs_df)

Arguments

orthologs_df

dataframe. orthologs with genomic coordinates loaded by load_orthologs()

Value

dataframe composed of details for each detected syntenic block of genes. It contains the following columns : sp1.Chr, sp1.Start, sp1.End, sp2.Chr, sp2.Start, sp2.End, size, sp1.IDs, sp2.IDs

See Also

load_orthologs()

Examples

# basic usage of get_syntenic_genes :

orthologs_table <- system.file("extdata","my_orthologs.tab",package="macrosyntR")

my_orthologs <- read.table(orthologs_table,header=TRUE)
                               
my_syntenic_block_of_genes <- get_syntenic_genes(my_orthologs)

macrosyntR documentation built on Nov. 14, 2023, 5:09 p.m.