Setup: Setup Seurat object
In nukappa/seurat_v2: Seurat : R toolkit for single cell genomics

Setup and initialize basic parameters of the Seurat object

Setup(object, project, min.cells = 3, min.genes = 1000, is.expr = 0,
  do.logNormalize = T, total.expr = 10000, do.scale = TRUE,
  do.center = TRUE, names.field = 1, names.delim = "_",
  meta.data = NULL, save.raw = TRUE)

`object`	Seurat object
`project`	Project name (string)
`min.cells`	Include genes with detected expression in at least this many cells
`min.genes`	Include cells where at least this many genes are detected
`is.expr`	Expression threshold for 'detected' gene
`do.logNormalize`	whether to normalize the expression data per cell and transform to log space.
`total.expr`	scale factor in the log normalization
`do.scale`	In object@scale.data, perform row-scaling (gene-based z-score)
`do.center`	In object@scale.data, perform row-centering (gene-based centering)
`names.field`	For the initial identity class for each cell, choose this field from the cell's column name
`names.delim`	For the initial identity class for each cell, choose this delimiter from the cell's column name
`meta.data`	Additional metadata to add to the Seurat object. Should be a data frame where the rows are cell names, and the columns are additional metadata fields
`save.raw`	TRUE by default. If FALSE, do not save the unmodified data in object@raw.data which will save memory downstream for large datasets