FindMyFriends (version 1.2.2)

.loadPgExample: Load an example pangenome

Description

This function loads an example pangenome at various stages of calculation, useful for examples and tests.

Usage

.loadPgExample(lowMem = FALSE, geneLoc = FALSE, withGroups = FALSE, withNeighborhoodSplit = FALSE, withParalogues = FALSE)

Arguments

lowMem

logical. Should the returned object inherit from pgLM

geneLoc

logical. Should the returned object inherit from pgVirtualLoc

withGroups

logical. Should gene groups be defined

withNeighborhoodSplit

logical. Should neighborhoodsplitting have been performed

withParalogues

logical. Should paralogue linking have been performed

Value

A pgVirtual subclass object to the specifications defined

Examples

# Load standard (pgFull)
.loadPgExample()

# Use pgLM
.loadPgExample(lowMem=TRUE)

# Create with pgVirtualLoc subclass (here pgFullLoc)
.loadPgExample(geneLoc=TRUE)

# Create with grouping information
.loadPgExample(withGroups=TRUE)

# Create with gene groups split by neighborhood (pgVirtualLoc implied)
.loadPgExample(withNeighborhoodSplit=TRUE)

# Create with paralogue links
.loadPgExample(withGroups=TRUE, withParalogues=TRUE)