initVATEntity: initialize VAT Entity

In HuobinTan/scVAT: Single Cell Visualization Analysis Toolkit

Description

initialize VAT Entity

Usage

initVATEntity(data.raw, title = "VAT", min.genes = 0, min.cells = 0,
  cell.scale = FALSE, scale.factor = 0, log.trans = TRUE,
  pseudocount = 1, verbose = TRUE)

Arguments

data.raw	data matrix
title	dataset name
min.genes	Include cells where more than this many genes are detected, default 0
min.cells	Include genes where more than this many cells are detected, default 0
cell.scale	whether or not normalizing by library size, default FALSE
scale.factor	multiple factor for cell.scale, default 0, using the mean for library size
log.trans	whether or not log-transform (log(p+pseudocount)), default TRUE
verbose	whether or not printing verbose, default TRUE
pseducount	pseducount for log-transform, default 1

Examples

vat <- initVATEntity(data.raw = data, title="VAT")

vat <- initVATEntity(data, title="VAT", min.genes = 0, min.cells = 3, cell.scale = TRUE)

HuobinTan/scVAT documentation built on May 31, 2019, 2:20 p.m.