gM: gM

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

gM

Description

gMatrix instantiator

Usage

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

Arguments

gr	GRanges around which to build a gMatrix or gPair object to sum
dat	data.table of $i and $j indexing gr and field $value OR a vector valued expression involving terms i and j that will be applied to expand.grid
outer	character scalar field of gr that will be used to generate an "outer product" of gr with itself, which given vector x for numerics will make each gmatrix entry equal to x_i*x_j and for character vector or factor fields will make each vector equal to x_i == x_j
field	if gr is a gPair then field can be a character that specifies a gPair metadata numeric or integer metadata field that will be used as weights to sum the gPair objects
full	logical flag whether to explicitly "fill" missing entries in provided data.table (default = FALSE)
fill	value with which to fill missing values (default 0)
agg.fun	default function with which to aggregate values, this function should take a vector and na.rm = TRUE and return a scalar
na.rm	default na.rm argument to agg.fun

Value

A new gMatrix object

Author(s)

Marcin Imielinski

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