Seurat (version 1.4.0)

Setup: Setup Seurat object

Description

Setup and initialize basic parameters of the Seurat object

Usage

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)

Arguments

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

Value

Seurat object. Fields modified include object@data, object@scale.data, object@data.info, object@ident