rank.de.gene: get gene ranking table from obj
In Japrin/sscClust: simpler single cell RNAseq data clustering

rank.de.gene

R Documentation

get gene ranking table from obj

Description

get gene ranking table from obj

Usage

rank.de.gene(
  obj,
  group = "pca.SNN.kauto",
  sort.by = "median.rank",
  weight.adj = NULL,
  group.2nd = NULL,
  mode.collapse = "comb",
  th.adj.P = 0.01,
  th.dprime = 0.15,
  ncores = 8
)

Arguments

`obj`	object; object of `singleCellExperiment` class
`group`	character; columan name in colData(obj)
`sort.by`	character; by which to sort the genes [default: "median.rank"]
`weight.adj`	character; column of obj, used to adjust weight [default: NULL]
`group.2nd`	character; column of obj, used for collapse [default: NULL]
`mode.collapse`	character; collapse method. one of "min", "comb" [default: "comb"]
`th.adj.P`	double; threshold [default: 0.01]
`th.dprime`	double; threshold [default: 0.15]
`ncores`	integer; number of CPU cores to use. (default: 8)