downsample_matrix: downsample matrix by cluster or completely random

In rnabioco/clustifyr: Classifier for Single-cell RNA-seq Using Cell Clusters

downsample matrix by cluster or completely random

Description

downsample matrix by cluster or completely random

Usage

downsample_matrix(
  mat,
  n = 1,
  keep_cluster_proportions = TRUE,
  metadata = NULL,
  cluster_col = "cluster"
)

Arguments

mat	expression matrix
n	number per cluster or fraction to keep
keep_cluster_proportions	whether to subsample
metadata	data.frame or vector containing cluster assignments per cell. Order must match column order in supplied matrix. If a data.frame provide the cluster_col parameters.
cluster_col	column in metadata with cluster number

Value

new smaller mat with less cell_id columns

Examples

set.seed(42)
mat <- downsample_matrix(
    mat = pbmc_matrix_small,
    metadata = pbmc_meta$classified,
    n = 10,
    keep_cluster_proportions = TRUE
)
mat[1:3, 1:3]

rnabioco/clustifyr documentation built on April 23, 2024, 9:57 a.m.