binarizeExp: binarize the expression value using the distribution

In Japrin/sscClust: simpler single cell RNAseq data clustering

binarize the expression value using the distribution

Description

binarize the expression value using the distribution

Usage

binarizeExp(
  x,
  out.prefix = NULL,
  G = NULL,
  topNAsHi = 1,
  e.TH = NULL,
  e.name = "Exp",
  verbose = F,
  draw.CI = T,
  zero.as.low = T,
  run.extremevalue = F,
  zero.notUsed = F,
  my.seed = 9997,
  ...
)

Arguments

x	object; vector
out.prefix	character; output prefix [default: NULL]
G	integer; number of components [default: NULL]
topNAsHi	integer; treat this number of top components as high;if it's zero, components with mean larger than 0 are high [default: 1]
e.TH	double; for plot purpose: comparing the components with the user defined threhold [default: NULL]
e.name	character; name of the expression metric [default: "Exp"]
verbose	logical; [default: F]
draw.CI	logical; [default: T]
zero.as.low	logical; [default: T]
run.extremevalue	logical; [default: F]
zero.notUsed	logical; [default: F]
my.seed	integer; [default: 9997]
...	parameters passed to plot.densityMclust

Details

use mixture model to classify each data point. If G is null, the largest component is corresponding to binarized expression 1, and other components are corresponding to binarized expressed 0.

Japrin/sscClust documentation built on May 23, 2024, 7:12 a.m.