ChromunityObj: Chromunity object

In mskilab/chromunity: Discovery of communities in Pore-C concatemers

Chromunity object

Description

Vectorized object that stores the output of chromunity analysis and can be inputted into annotate / synergy functions. The main accessors are $binsets and $concatemers which each return GRanges linked through a chromunity id $chid field

Chromunities can be subsetted, concatenated. Concatenation will result in deduping any $chid that are present in two inputs.

Methods

Public methods

• ChromunityObj$new()

• ChromunityObj$subset()

• ChromunityObj$print()

• ChromunityObj$gtrack()

• ChromunityObj$gm()

• ChromunityObj$clone()

---

Method new()

Usage

ChromunityObj$new(
  binsets = GRanges(),
  concatemers = GRanges(),
  meta = data.table(),
  verbose = TRUE
)

---

Method subset()

Usage

ChromunityObj$subset(ix, ...)

---

Method print()

Usage

ChromunityObj$print(...)

---

Method gtrack()

Usage

ChromunityObj$gtrack(
  name = "",
  binsets = TRUE,
  concatemers = TRUE,
  heatmap = FALSE,
  binsize = 10000,
  clim = NA,
  ...
)

---

Method gm()

Usage

ChromunityObj$gm(binsize = 5000)

---

Method clone()

The objects of this class are cloneable with this method.

Usage

ChromunityObj$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

mskilab/chromunity documentation built on April 12, 2024, 10:35 a.m.