GxG: GxG

In mskilab/GxG: GxG: Genomic matrices and pairwise genomic features based on GenomicRanges and data.table

GxG

Description

Matrices and pairwise features in a GenomicRanges / data.table framework

Copyright (C) 2018 Marcin Imielinski

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.

Github: https://github.com/mskilab/GxG

Methods

Public methods

• gMatrix$new()

• gMatrix$disjoin()

• gMatrix$sweep()

• gMatrix$metaset()

• gMatrix$annotate()

• gMatrix$clusters()

• gMatrix$transform()

• gMatrix$set()

• gMatrix$agg()

• gMatrix$merge()

• gMatrix$subset()

• gMatrix$gtrack()

• gMatrix$peaks()

• gMatrix$hicpro()

• gMatrix$pack()

• gMatrix$print()

• gMatrix$clone()

---

Method new()

Usage

gMatrix$new(
  gr = NULL,
  dat = NULL,
  field = NULL,
  fill = 0,
  full = NULL,
  na.rm = TRUE,
  agg.fun = sum,
  lower.tri = FALSE
)

---

Method disjoin()

Usage

gMatrix$disjoin(gr = NULL)

---

Method sweep()

Usage

gMatrix$sweep(vec, FUN = "-", MARGIN = c(1))

---

Method metaset()

Usage

gMatrix$metaset(...)

---

Method annotate()

Usage

gMatrix$annotate(y)

---

Method clusters()

Usage

gMatrix$clusters(mode = "louvain", gpair = TRUE)

---

Method transform()

Usage

gMatrix$transform(FUN, ...)

---

Method set()

Usage

gMatrix$set(val, gr1 = NULL, gr2 = NULL)

---

Method agg()

Usage

gMatrix$agg(gr = NULL, FUN = private$pagg.fun, weighted = FALSE)

---

Method merge()

Usage

gMatrix$merge(
  gmats = NULL,
  FUN = self$agg.fun,
  simplify = FALSE,
  mc.cores = 1,
  verbose = FALSE
)

---

Method subset()

Usage

gMatrix$subset(gr1 = NULL, gr2 = NULL)

---

Method gtrack()

Usage

gMatrix$gtrack(
  name = "",
  colormap = c("white", "red", "black"),
  clim = NA,
  cmap.min = NA,
  cmap.max = NA,
  quantile = 0.01,
  max.ranges = 3000,
  ...
)

---

Method peaks()

Usage

gMatrix$peaks(reverse = FALSE, full = FALSE)

---

Method hicpro()

Usage

gMatrix$hicpro(file, verbose = TRUE)

---

Method pack()

Usage

gMatrix$pack(seqname = "1")

---

Method print()

Usage

gMatrix$print()

---

Method clone()

The objects of this class are cloneable with this method.

Usage

gMatrix$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

mskilab/GxG documentation built on April 12, 2025, 5:32 p.m.