getRDS: reduce expression space

In minzheguo/SLICE: Determining Cell Differentiation and Lineage based on Single Cell Entropy

reduce expression space

Description

perform dimesion reduction using PCA using the expression profiles of genes satisfied the following criteria: included in the "gene.use", had log2 expression variance greater than min.var, and expressed (>1) in at least "min.cells" number of cells.

Usage

getRDS(
  object,
  genes.use = NULL,
  method = "pca",
  num_dim = 2,
  log.base = 2,
  do.center = TRUE,
  do.scale = FALSE,
  use.cor = T,
  min.var = 0.5,
  min.cells = 3,
  ...
)

Arguments

object	slice object
genes.use	The set of genes whose expression will be used for dimension reduction; if NULL, set to all genes
method	The method for dimension reduction; currently, only support "pca"; more options will be integrated soon
num_dim	The number of dimensions to be extracted
log.base	The base of logarithm
do.center	If TRUE, substract row-mean from each value
do.scale	If TRUE, divide by row standard deviation
use.cor	If TRUE, use Pearson's correlation matrix as input to prcomp function
min.var	The minimum expression variance for a gene to be included in dimension reduction
min.cells	The minimum number of expressed cells for a gene to be included in dimension reduction

Value

updated slice object with reduced dimensions in the "rds" slot, the first two components are also used to set the "vds" slot for visualization.

minzheguo/SLICE documentation built on June 5, 2023, 11:56 a.m.