compute_macrosynteny {macrosyntR} | R Documentation |
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)
[Package macrosyntR version 0.3.3 Index]