chromoplexy: Find Chromoplexy chains

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

Find Chromoplexy chains

Description

Finds chromoplexy chains as clusters of "long distance" junctions that each span at least min.span (i.e. distant regions on the reference) have junctions nearby ie within max.dist. We filter to chains that have at least min.num footprints on the genome and involve at least min.num long distance junctions. We keep track of how many "other" (non small dup and non small del) junctions there are in the vicinity for downstream filtering.

Usage

chromoplexy(
  gg,
  min.span = 1e+07,
  max.dist = 10000,
  min.num = 3,
  max.cn = 3,
  footprint.width = 1e+06,
  ignore.small.dups = TRUE,
  ignore.small.dels = TRUE,
  max.small = 50000,
  mark = FALSE,
  mark.col = "purple"
)

Arguments

gg	gGraph
min.span	minimimum span to define a "long distance" junction and also the span by which major footprints of the event must be separated Default: 1e7
max.dist	maximum distance allowed in edge clusters Default: 1e4
min.num	minimum number of junctions and major footprints that define a chromoplexy Default: 3
max.cn	max copy number before filter Default: 3
footprint.width	padding around which to define the footprint of an event, note that the outputted footprint only includes the chromoplexy junction breakpoints. Default: 1e6
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	mark chromoplexies. Default:FALSE
mark.col	color to mark chromoplexies. Default: purple

Details

For more details on what chromoplexies are and visualized: Chromoplexy and TICs

Value

gGraph with $meta$chromoplexy annotated with chromoplexy event metadata and edges labeled with $chromoplexy id or NA if the edge does not belong to a chromoplexy

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