basicP2proc {pagoda2}

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