compute_macrosynteny: Compute significant macrosynteny blocks

In macrosyntR: Draw Ordered Oxford Grids and Chord Diagrams

Compute significant macrosynteny blocks

Description

This is a function to generate the contingency table of an orthologs dataframe and apply fischer test to calculate the significant associations. It outputs a dataframe shaped as following : sp1.Chr,sp2.Chr,a,pval,significant,pval_adj

Usage

compute_macrosynteny(orthologs_df, pvalue_threshold = 0.001)

Arguments

orthologs_df	dataframe. orthologs with genomic coordinates loaded with load_orthologs()
pvalue_threshold	numeric. threshold for significancy. (default equals 0.001)

Value

A dataframe object

Examples

# basic usage of compute_macrosynteny : 

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

my_orthologs <- read.table(orthologs_table,header=TRUE)
                               
my_macrosynteny <- compute_macrosynteny(my_orthologs)

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