downsampling {CIDER}R Documentation

Downsampling cells

Description

Downsampling cells from each group for IDER-based similarity calculation.

Usage

downsampling(
  metadata,
  n.size = 35,
  seed = 12345,
  include = FALSE,
  replace = FALSE,
  lower.cutoff = 3
)

Arguments

metadata

Data frame. It includes at least 2 columns, label and batch. Each row corresponds to one cell. Required.

n.size

Numeric. The number of cells used in each group. (Default: 35)

seed

Numeric. Seed used to sample. (Default: 12345)

include

Boolean. Using 'include = TRUE' to include the group smaller than required size. (Default: FALSE)

replace

Boolean. Using 'replace = TRUE' if the group is smaller than required size and some cells will be repeatedly used. (Default: FALSE)

lower.cutoff

Numeric. The minimum size of groups to keep. (Default: 3)

Value

A numeric list of which cells will be kept for downstream computation.


[Package CIDER version 0.99.0 Index]