gWalk: gWalk

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

gWalk

Description

gWalk object

Methods

Public methods

• gWalk$new()

• gWalk$set()

• gWalk$subset()

• gWalk$dts()

• gWalk$fix()

• gWalk$rep()

• gWalk$print()

• gWalk$json()

• gWalk$eval()

• gWalk$disjoin()

• gWalk$simplify()

• gWalk$mark()

• gWalk$fitcn()

• gWalk$gtrack()

• gWalk$clone()

---

Method new()

Usage

gWalk$new(
  snode.id = NULL,
  sedge.id = NULL,
  grl = NULL,
  graph = NULL,
  meta = NULL,
  circular = NULL,
  disjoin = FALSE,
  drop = FALSE
)

---

Method set()

Usage

gWalk$set(...)

---

Method subset()

Usage

gWalk$subset(i)

---

Method dts()

Usage

gWalk$dts(ix = 1:self$length, makelists = TRUE)

---

Method fix()

Usage

gWalk$fix(pattern = NULL, replacement = NULL, drop = TRUE, seqlengths = NULL)

---

Method rep()

Usage

gWalk$rep(times)

---

Method print()

Usage

gWalk$print()

---

Method json()

Usage

gWalk$json(
  filename = ".",
  save = TRUE,
  verbose = FALSE,
  annotations = NULL,
  nfields = NULL,
  efields = NULL,
  stack.gap = 1e+05,
  include.graph = TRUE,
  settings = list(y_axis = list(title = "copy number", visible = TRUE)),
  cid.field = NULL,
  no.y = FALSE
)

---

Method eval()

Usage

gWalk$eval(x, node, edge)

---

Method disjoin()

Usage

gWalk$disjoin(
  gr = NULL,
  graph = NULL,
  by = NULL,
  collapse = TRUE,
  na.rm = TRUE,
  avg = FALSE,
  sep = ",",
  FUN = default.agg.fun.generator(na.rm = na.rm, sep = sep, avg = avg)
)

---

Method simplify()

Usage

gWalk$simplify(
  by = NULL,
  na.rm = TRUE,
  avg = FALSE,
  sep = ",",
  FUN = default.agg.fun.generator(na.rm = na.rm, sep = sep, avg = avg)
)

---

Method mark()

Usage

gWalk$mark(...)

---

Method fitcn()

Usage

gWalk$fitcn(
  trim = TRUE,
  weight = NULL,
  obs.mat = NULL,
  verbose = FALSE,
  min.alt = TRUE,
  edgeonly = FALSE,
  evolve = FALSE,
  n.sol = 2
)

---

Method gtrack()

Usage

gWalk$gtrack(name = NULL, stack.gap = 1e+05, ...)

---

Method clone()

The objects of this class are cloneable with this method.

Usage

gWalk$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

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