ExampleStreptomycesData: Example EvoWeaver Input Data from _Streptomyces_ Species

In npcooley/SynExtend: Tools for Working With Synteny Objects

Example EvoWeaver Input Data from Streptomyces Species

Description

Data from Streptomyces species to test EvoWeaver functionality.

Usage

data("ExampleStreptomycesData")

Details

This dataset contains a number of Clusters of Orthologous Genes (COGs) and a species tree for use with EvoWeaver. This dataset showcases an example of using EvoWeaver with a list of vectors. Entries in each vector are formatted correctly for use with co-localization prediction. Each COG i contains entries of the form a_b_c, indicating that the gene was found in genome a on chromosome b, and was at the c'th location. The original dataset is comprised of 301 unique genomes.

Value

The data contain two elements, Genes and Tree. Genes is a list of presence/absence vectors in the input required for EvoWeaver. Tree is a species tree used for additional input.

See Also

EvoWeaver

Examples

exData <- get(data("ExampleStreptomycesData"))
ew <- EvoWeaver(exData$Genes)
# Subset isn't necessary but is faster for a working example
predict(ew, Subset=1:10, MySpeciesTree=exData$Tree)

npcooley/SynExtend documentation built on May 2, 2024, 7:28 p.m.