Usage
setup(object, project, min.cells = 3, min.genes = 2500, is.expr = 1, do.scale = TRUE, do.center = TRUE, names.field = 1, names.delim = "_", meta.data = NULL, save.raw = TRUE, ...)
Arguments
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.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
...
Additional arguments, not currently used.