Averaged feature expression by identity class
Returns averaged expression values for each identity class
AverageExpression( object, assays = NULL, features = NULL, return.seurat = FALSE, group.by = "ident", add.ident = NULL, slot = "data", verbose = TRUE, ... )
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 |
Categories for grouping (e.g, ident, replicate, celltype); 'ident' by default |
add.ident |
(Deprecated) Place an additional label on each cell prior to pseudobulking (very useful if you want to observe cluster pseudobulk values, separated by replicate, for example) |
slot |
Slot(s) to use; if multiple slots are given, assumed to follow the order of 'assays' (if specified) or object's assays |
verbose |
Print messages and show progress bar |
... |
Arguments to be passed to methods such as |
If slot is set to 'data', this function assumes that the data has been log
normalized and therefore feature values are exponentiated prior to averaging
so that averaging is done in non-log space. Otherwise, if slot is set to
either 'counts' or 'scale.data', no exponentiation is performed prior to
averaging
If return.seurat = TRUE and slot is not 'scale.data', averaged values
are placed in the 'counts' slot of the returned object and the log of averaged values
are placed in the 'data' slot. ScaleData is then run on the default assay
before returning the object.
If return.seurat = TRUE and slot is 'scale.data', the 'counts' slot is left empty,
the 'data' slot is filled with NA, and 'scale.data' is set to the aggregated values.
Returns a matrix with genes as rows, identity classes as columns.
If return.seurat is TRUE, returns an object of class Seurat.
data("pbmc_small")
head(AverageExpression(object = pbmc_small))Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.