run_dim_red: Run DR

In Yutong441/TBdev: Infer a Trophoblast Developmental Trajectory

Description

Run DR

Usage

run_dim_red(
  x,
  assay = NULL,
  select_cells = NULL,
  feature_num = 2000,
  find_var_features = FALSE,
  save_mem = NULL,
  normalize = FALSE,
  var_scale = FALSE,
  pca_features = NULL,
  run_diff_map = FALSE,
  run_umap = TRUE,
  cluster = TRUE,
  cluster_res = 0.5,
  neighbor_dim = 10
)

Arguments

assay	assay to use for dimensionality reduction
select_cells	run PCA on a selected population of cells; should be a boolean vector
feature_num	how many variably expressed genes to compute
find_var_features	whether to run variable gene analysis
save_mem	for large matrices whether the entire matrix should be stored, or simply storing the VariableFeatures
normalize	whether to normalize the data
var_scale	the variable features only to reduce memory
pca_features	run PCA on a selected list of genes, should be a character vector
run_diff_map	whether to run diffusion map using the package destiny. Depending on the dataset, this may take several minutes
run_umap	whether to run umap
cluster	whether to perform clustering as well

Value

a Seurat object

Yutong441/TBdev documentation built on Dec. 18, 2021, 8:22 p.m.