Cell type annotation with Seurat::AddModuleScore
cell_annot_custom.RdThis function performs automatic annotation of clusters in a Seurat object, based on a provided list of markers and cellular populations names. This function uses Seurat::AddModuleScore to attribute a score to each cell. Then, it gives to the cell to cell type corresponding to the highest score.
Usage
cell_annot_custom(
sobj,
assay = "RNA",
layer_use = "data",
newname = "annotation",
markers = markers,
use_negative = FALSE,
add_score = FALSE,
prefix = "score_",
seed = 1337L,
verbose = TRUE
)Arguments
- sobj
A Seurat object (no default)
- assay
CHARACTER : on which assay from sobj to perform cell type annotation ? (default to 'RNA')
- layer_use
CHARACTER : on which layer in the assay to perform cell type annotation (default to 'data')
- newname
CHARACTER : name for the new column in metadata (default to 'annotation')
- markers
LIST : a named list containing markers for each population (no default)
- use_negative
LOGICAL : whether to use all markers as negative markers for each cell type or not, in the definition of cell type (default to FALSE)
- add_score
LOGICAL : whether to add the columns containing scores to metadata in sobj (default to FALSE)
- prefix
CHARACTER : if add_score is set to TRUE, the prefix for new column names in metadata. For example, if a population type is called "pop1", which names to give to the new column in metadata containing score ? If prefix is "score_", then new column will be "score_pop1" (default to "score_")
- seed
INTEGER : the seed to be used by Seurat::AddModuleScore (default to 1337L)
- verbose
LOGICAL : whether to print messages or not (default to TRUE)