dup: Find duplications and pyrgos

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

Find duplications and pyrgos

Description

Calls simple duplications (dup) and pyrgo, which are clusters or "towers" of overlapping duplications

Duplications are defined as having low junction copy number and connect two nodes of low junction copy number (with cn and jcn thresholds provided as parameters). Simple duplications have no other overlapping junctions in their shadow. Pyrgo have a min.count and are also outliers (<fdr.thresh) in a negative binomial modup that incorporates the regional (non-DUP) junction count in tile.width genomic bins (set to 1 Mbp by default).

Note: Not all DUP-like junctions will be called a dup or pyrgo.

Usage

dup(
  gg,
  fdr.thresh = 0.5,
  tile.width = 1e+06,
  jcn.thresh = 1,
  min.count = 2,
  return.fish = FALSE,
  mark = FALSE,
  mark.col = "purple",
  min.width = 10000,
  max.width.flank = 10000,
  max.width = 1e+07
)

Arguments

gg	gGraph with $cn field annotated on nodes and edges
fdr.thresh	False discovery rate threshold for fishook calculated events. Default: 0.5
tile.width	bin width to use when computing duplication clustering Default: 1e6
jcn.thresh	edge copy number threshold to call a duplication in ploidy units. Default: 1
min.count	minimum number of overlapping duplications to constitute a pyrgo, includes the tile.width. Default 2
return.fish	parameter to return FishHook::Fish() output. Default: False
mark	color duplication events. Default: False
mark.col	color of duplication events. Default: purple
min.width	min width of duplications to consider for pyrgo. Default: 1e4
max.width.flank	max width flank each side of class DEL-like to consider. Default: 1e4
max.width	max width of duplications to consider for pyrgo. Default: 1e7

Details

For more details on how to run the function and examples: Duplications & Pyrgo

Value

gGraph with nodes and edges annotated with $dup and $pyrgo metadata field, and data.tables $meta$pyrgo and $meta$set with event level statistics.

If return.fish = TRUE, returns FishHook::Fish() output.

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