Seurat (version 2.1.0)

CreateSeuratObject: Initialize and setup the Seurat object

Description

Initializes the Seurat object and some optional filtering

Usage

CreateSeuratObject(raw.data, project = "SeuratProject", min.cells = 0,
  min.genes = 0, is.expr = 0, normalization.method = NULL,
  scale.factor = 10000, do.scale = FALSE, do.center = FALSE,
  names.field = 1, names.delim = "_", meta.data = NULL, save.raw = TRUE,
  display.progress = TRUE)

Arguments

raw.data

Raw input data

project

Project name (string)

min.cells

Include genes with detected expression in at least this many cells. Will subset the raw.data matrix as well. To reintroduce excluded genes, create a new object with a lower cutoff.

min.genes

Include cells where at least this many genes are detected.

is.expr

Expression threshold for 'detected' gene. For most datasets, particularly UMI datasets, will be set to 0 (default). If not, when initializing, this should be set to a level based on pre-normalized counts (i.e. require at least 5 counts to be treated as expresesd) All values less than this will be set to 0 (though maintained in [e-mail]).

normalization.method

Method for cell normalization. Default is no normalization. In this case, run NormalizeData later in the workflow. As a shortcut, you can specify a normalization method (i.e. LogNormalize) here directly.

scale.factor

If normalizing on the cell level, this sets the scale factor.

do.scale

In [e-mail], perform row-scaling (gene-based z-score). FALSE by default. In this case, run ScaleData later in the workflow. As a shortcut, you can specify do.scale = TRUE (and do.center = TRUE) here.

do.center

In [e-mail], 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 [e-mail] which will save memory downstream for large datasets

display.progress

display progress bar for normalization and/or scaling procedure.

Value

Returns a Seurat object with the raw data stored in [e-mail]. object@data, [e-mail], object@ident, also initialized.

Examples

# NOT RUN {
pbmc_raw <- read.table(
  file = system.file('extdata', 'pbmc_raw.txt', package = 'Seurat'),
  as.is = TRUE
)
pbmc_small <- CreateSeuratObject(raw.data = pbmc_raw)
pbmc_small

# }