loadPgExample: Load an example pangenome

In FindMyFriends: Microbial Comparative Genomics in R

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)

FindMyFriends documentation built on Nov. 8, 2020, 6:46 p.m.