rank.de.gene: get gene ranking table from obj

View source: R/integrate.R

rank.de.geneR 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)

Details

rank genes

Value

a gene table


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