chromothripsis: Find Chromothripsis

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

Find Chromothripsis

Description

Finds chromothripsis as clusters of >= min.seg segments and >= min.jun junctions, clusters defined as clusters of segs with <= max.seg.width spread across <= max.major footprints with cn <= max.cn and cn amplitude cn <= max.cn.amplitude and also fractional width distribution consistent with dirichlet orientation distribution consistent with Uniform and window distribution (if multiple windows) consistent with Uniform.

"Major" footprints are defined as reduced footprints that have width >= min.major.width.

We may also allow a number of (<= min.majo) "minor" footprints (e.g. templated insertions) each <= min.major.width to prevent clusters from being thrown out because certain TI junctions are mapped in multiple parts.

Usage

chromothripsis(
  gg,
  min.seg = 8,
  min.jun = 7,
  max.cn = 4,
  max.cn.amplitude = 3,
  max.major = 4,
  min.major.width = 1e+05,
  max.minor = 2,
  min.p.orientation = 0.001,
  min.stack = 3,
  min.mean.stack = 3,
  fbi.thresh = 50000,
  remove.small.junctions = TRUE,
  small.junction.thresh = 10000,
  scale.to.ploidy = TRUE,
  mark = TRUE,
  mark.col = "purple"
)

Arguments

gg	gGraph
min.seg	minimum number of segments in a CT. Default: 8
min.jun	minimum number of junctions in a CT. Default: 7
max.cn	max CN of a CT. Default: 4
max.major	max number of "major" footprints of CT with width >= min.major.width. Default: 4
min.major.width	width threshold defining a major footprint. Default: 1e5
max.minor	max number of "minor" footprints of CT with width < min.major.width. Default: 2
min.p.orientation	minimum pvalue orientation needed in cluster to keep in cluster stats. Default: 0.001
min.stack	minimum stack threshold to make make clusters around ALT junction shadows. Default: 3
min.mean.stack	average number of "stacks" in event treating each junction span as a GRanges. Default: 2
fbi.thresh	Default: 5e4
remove.small.junctions	removes small junctions found Default: TRUE
small.junction.thresh	threshold for a junction to be considered small Default: 1e4
scale.to.ploidy	Scale to ploidy. if TRUE will double thresholds for amplitude and CN when ploidy is > 3.5 Default: True
mark	logical flag to color eventsDefault: True
mark.col	color of event Default: purple
max.cn.ampltitude	max difference between top and bottom CN in a CT. Default: 3

Details

for more details on chromothripsis: Chromothripsis

Value

gGraph with nodes and edges annotated with integer chromothripsis event or NA and metadata showing some statistics for the returns chromothripsis events

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