integrate_synteny: Integrate syntenic positions across multiple genomes

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

Integrate syntenic positions across multiple genomes

Description

integrate_synteny Internal functions to connect syntenic positions for riparian plotting and interpolated gene order calculation for placement of syntenic pan-genes.

interp_synPos pipes data to interp_approx and combines across genomes

phase_blks splits blocks so that each is anchored to a single reference genome chromosome, which allows the construction of default riparian plots

nophase_blks simple wrapper for calc_blkCoords so that block coordinates are calculated across all combination of genomes.

calc_blkCoords from a hits object, determine block coordinates, orientation and membership

Usage

interp_synPos(gsParam, verbose = TRUE)

phase_blks(
  gsParam,
  refGenome,
  useRegions,
  blkSize = 5,
  synBuff = 100,
  refChr = NULL,
  refStartBp = NULL,
  refEndBp = NULL
)

nophase_blks(gsParam, useRegions, blkSize = 5)

calc_blkCoords(hits, mirror = FALSE)

Arguments

gsParam	A list of genespace parameters created by init_genespace.
verbose	logical, should updates be printed to the console?
refGenome	Character string specifying the reference genome to use
useRegions	Logical, should regions be used instead of blocks?
blkSize	see init_genesapce
synBuff	see init_genesapce
refChr	string matching chromosome IDs in refGenome
refStartBp	physical (bp) region start coordinate on refChr
refEndBp	physical (bp) region end coordinate on refChr
hits	data.table with hits (see read_synHits)
mirror	logical, should the block coordinates be mirrored between query and target genomes

Details

Functions here should not be called directly by the user except if customizing riparian plots.

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