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)Seurat object
Project name (string)
Include genes with detected expression in at least this many cells
Include cells where at least this many genes are detected
Expression threshold for 'detected' gene
whether to normalize the expression data per cell and transform to log space.
scale factor in the log normalization
In object@scale.data, perform row-scaling (gene-based z-score)
In object@scale.data, perform row-centering (gene-based centering)
For the initial identity class for each cell, choose this field from the cell's column name
For the initial identity class for each cell, choose this delimiter from the cell's column name
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
TRUE by default. If FALSE, do not save the unmodified data in object@raw.data which will save memory downstream for large datasets
Seurat object. Fields modified include object@data, object@scale.data, object@data.info, object@ident