jhom: wrapper around GxG homeology for junctions

In mskilab/skitools: Various mskilab R utilties

wrapper around GxG homeology for junctions

Usage

jhom(
  event,
  pad = 100,
  thresh = 2,
  stride = 1,
  pad2 = 5,
  flip = FALSE,
  stats = FALSE,
  mc.cores = 1,
  anchor = TRUE,
  mat = FALSE
)

Arguments

event	Junction object around which to compute homeology
pad	padding to put around breakpoint window
thresh	maximum string distance threshold for calling a bin homeologous
pad2	pad to put around an output bin in order to measure homeology
flip	flag whether to measure homeology with bins and their reverse complements
stats	flag whether to return stats or gMatrix (default)
mc.cores	integer number of cores [1]
anchor	logical flag whether to return homeology results around native (inputted) coordinates or Anchored coordinates [TRUE]
mat	logical whether to return results as a mat [FALSE] or gMatrix

Value

list of gMatrix objects (if stats = FALSE) and data.table of homeology stats (if stats = TRUE)

Author(s)

Marcin Imielinski

mskilab/skitools documentation built on Aug. 31, 2023, 1:13 p.m.