tic: Find templated insertion chains (tics)

In mskilab/gGnome: gGnome: reference based assembly graph for analyzing rearranged genomes

Find templated insertion chains (tics)

Description

Finds "clean" templated insertion chains eg paths and cycles of junctions with span > min.span by first identifying jbp pairs within max.insert distance for which the "left" jbp is + and "right" jbp is - (in reference coordinates) excluding any jbp that have more than one ALT jbp (or optionally loose ends) with min.cushion distance. These remaining jbp pairs are then combined into a graph, and connected components in that graph are scraped for paths and cycles, which are marked on the graph and added as metadata to the outputted gGraph.

Usage

tic(
  gg,
  max.insert = 50000,
  min.cushion = 5e+05,
  min.span = 1e+06,
  min.length = 2,
  ignore.loose.ends = TRUE,
  ignore.small.dups = TRUE,
  ignore.small.dels = TRUE,
  max.small = 50000,
  mark = FALSE,
  mark.col = "purple"
)

Arguments

gg	gGraph
max.insert	max insert to consider in a templated insertion Default: 5e5
min.cushion	minimum cushion between a TIC junction and any other nearby event (to ensure "clean" events), the bigger the cushion, the cleaner the calls Default: 5e5
min.span	min span for a TIC junction Default: 1e6
ignore.loose.ends	logical flag determining whether we ignore loose ends when filtering on min.cushion. Default: TRUE
ignore.small.dups	logical flag determining whether we ignore small dups when filtering on min.cushion. Default: True
ignore.small.dels	logical flag determining whether we ignore small dels when filtering on min.cushion. Default: True
max.small	threshold for calling a local dup or del "small" Default: 5e4
mark	Default: FALSE
mark.col	Default: purple

Details

For more detail on running tic and examples see the tutorial: tic

Value

gGraph with $meta annotated with gWalks corresponding to tic and tip and nodes and edges labeled with 'p1' through 'pk' for all k templated insertion paths and 'c1' through 'ck' for all k templated insertion cycles

mskilab/gGnome documentation built on May 8, 2024, 4:25 p.m.