syntenic_pangenes: generate syntenic pan-gene sets

In jtlovell/GENESPACE: Synteny- and orthology-constrained comparative genomics

generate syntenic pan-gene sets

Description

syntenic_pangenes Integrates interpolated gene order position with orthogroups to generate pan-gene sets across multiple genomes.

Usage

syntenic_pangenes(
  gsParam,
  refGenome,
  maxPlacePerChr = 2,
  minPropInterp2keep = 0.75
)

Arguments

gsParam	A list of genespace parameters. This should be created by init_genespace.
refGenome	character specifying the reference genome
maxPlacePerChr	integer specifying the maximum number of placements allowed on a single reference chromosome. This keeps things simpler in very messy synteny maps.
minPropInterp2keep	numeric specifying the minimum proportion of genes in an orthogroup with positions clustered into a specific location.

Details

formerly called 'pangenome' this function decomposes orthogroups and syntenic interpolated positions into a long-formatted pan-gene set. See query_pangenes to access this output.

jtlovell/GENESPACE documentation built on Jan. 25, 2025, 6:39 a.m.