Seurat already performs this operation as sparse matrix multiplication. scop preserves its complete parameter and object contract.
Usage
AggregateExpression(
object,
assays = NULL,
features = NULL,
return.seurat = FALSE,
group.by = "ident",
add.ident = NULL,
normalization.method = "LogNormalize",
scale.factor = 10000,
margin = 1,
verbose = TRUE,
...
)Arguments
- object
Seurat object
- assays
Which assays to use. Default is all assays
- features
Features to analyze. Default is all features in the assay
- return.seurat
Whether to return the data as a Seurat object. Default is FALSE
- group.by
Category (or vector of categories) for grouping (e.g, ident, replicate, celltype); 'ident' by default To use multiple categories, specify a vector, such as c('ident', 'replicate', 'celltype')
- add.ident
(Deprecated). Place an additional label on each cell prior to pseudobulking
- normalization.method
Method for normalization, see
NormalizeData- scale.factor
Scale factor for normalization, see
NormalizeData- margin
Margin to perform CLR normalization, see
NormalizeData- verbose
Print messages and show progress bar
- ...
Arguments to be passed to methods such as
CreateSeuratObject