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")

Format

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.

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.

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 Dec. 20, 2024, 4:03 p.m.