DUBStepR (version 1.2.0)

DUBStepR: DUBStepR - Obtain a list of feature genes to characterise cell types

Description

DUBStepR - Obtain a list of feature genes to characterise cell types

Usage

DUBStepR(
  input.data,
  min.cells = 0.05 * ncol(input.data),
  species = "human",
  optimise.features = TRUE,
  k = 10,
  num.pcs = 20,
  error = 0
)

Arguments

input.data

input gene expression matrix (genes x cells)

min.cells

minimum number of cells to filter genes out

species

species to use for gene filtering: "human" (default), "mouse" and "rat"

optimise.features

Determine optimal feature set using density index

k

number of nearest neighbours. Default is 10

num.pcs

number of principal components to represent sc data. Default is 20

error

Acceptable error margin for kNN computation. Default is 0, but is set to 1 for large datasets

Value

Returns optimal feature set

Examples

# NOT RUN {
res <- DUBStepR(input.data = pbmc_norm_small_data)

# }