straw: straw

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

straw

Description

Instantiates gMatrix from .hic object using straw API https://github.com/theaidenlab/straw/tree/master/R used to extract all of the data in length n query gr (note will do n choose 2 queries since straw only supports pairwise queries)

Usage

straw(
  hic,
  gr = NULL,
  norm = "NONE",
  type = "BP",
  res = 10000,
  mc.cores = 1,
  colormap = c("white", "red", "black"),
  ...
)

Arguments

hic	path to .hic file
gr	granges to query
norm	string specifying normalization to apply ("KR" (default), "NONE", VC")
type	"BP" vs "FRAG"
res	resolution to query (default 10kb)
mc.cores	parallelization to apply for query (useful when length(gr)>2)

Value

gMatrix

Author(s)

Marcin Imielinski Tuesday, Nov 07, 2017 04:43:52 PM - Julie: adding as.character()

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