basicP2proc: Perform basic 'pagoda2' processing, i.e. adjust variance,...

In pagoda2: Single Cell Analysis and Differential Expression

Perform basic 'pagoda2' processing, i.e. adjust variance, calculate pca reduction, make knn graph, identify clusters with multilevel, and generate largeVis and tSNE embeddings.

Description

Perform basic 'pagoda2' processing, i.e. adjust variance, calculate pca reduction, make knn graph, identify clusters with multilevel, and generate largeVis and tSNE embeddings.

Usage

basicP2proc(
  cd,
  n.cores = 1,
  n.odgenes = 3000,
  nPcs = 100,
  k = 30,
  perplexity = 50,
  log.scale = TRUE,
  trim = 10,
  keep.genes = NULL,
  min.cells.per.gene = 0,
  min.transcripts.per.cell = 100,
  get.largevis = TRUE,
  get.tsne = TRUE,
  make.geneknn = TRUE
)

Arguments

cd	count matrix whereby rows are genes, columns are cells.
n.cores	numeric Number of cores to use (default=1)
n.odgenes	numeric Number of top overdispersed genes to use (dfault=3e3)
nPcs	numeric Number of PCs to use (default=100)
k	numeric Default number of neighbors to use in kNN graph (default=30)
perplexity	numeric Perplexity to use in generating tSNE and largeVis embeddings (default=50)
log.scale	boolean Whether to use log scale normalization (default=TRUE)
trim	numeric Number of cells to trim in winsorization (default=10)
keep.genes	optional set of genes to keep from being filtered out (even at low counts) (default=NULL)
min.cells.per.gene	numeric Minimal number of cells required for gene to be kept (unless listed in keep.genes) (default=0)
min.transcripts.per.cell	numeric Minimumal number of molecules/reads for a cell to be admitted (default=100)
get.largevis	boolean Whether to caluclate largeVis embedding (default=TRUE)
get.tsne	boolean Whether to calculate tSNE embedding (default=TRUE)
make.geneknn	boolean Whether pre-calculate gene kNN (for gene search) (default=TRUE)

Value

a new 'Pagoda2' object

pagoda2 documentation built on June 24, 2024, 9:09 a.m.