get_AB: a shim function, mostly to feed plot_ABC()

In trichelab/velocessor: The world's dumbest single-cell RNA velocity calculator and loader

Description

binarize & TF-IDF SCE, then call boundaries requires a genome for the SCE or it will fail requires coordinates for the SCE or it will fail don't run this on thousands of cells ungrouped

Usage

get_AB(
  x,
  asy = "counts",
  chr = "chr3",
  res = 1e+05,
  boot = 10,
  minct = 1,
  mincl = 1,
  ...
)

Arguments

x	something that inherits from RangedSummarizedExperiment
asy	assay to feed compartmap ("counts"; see Details)
chr	what chromosome to work on ("chr3")
res	resolution for compartmap bins, in base pairs (1e5)
boot	how many bootstraps to run for compartmap (10)
minct	minimum number of counts to consider "nonzero" (see Details)
mincl	minimum number of cells to consider "nonzero" (see Details)
...	parameters to feed to getATACABsignal (e.g. group, cores, etc)

Details

The value "ratio" for asy means "unspliced / spliced" and is computed on the fly, for the purpose of identifying "unstable" regions of chromatin. It is not (repeat, NOT) ready for prime time, not least due to TF-IDF vs. LSI. That said, the value of min (which defaults to 1) plays an important role in determining which transcripts to consider: any transcript that does not have at least minct counts unspliced in at least mincl cells will not be considered in the resulting downstream analyses (which are subsetted to "nonzero" regions of chromatin for conformational modeling purposes).

Value

   AB signal

See Also

  compartmap::getATACABsignal

trichelab/velocessor documentation built on Jan. 5, 2022, 6:27 p.m.