Find Chromothripsis

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.

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

Value

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

Details

for more details on chromothripsis: Chromothripsis