runDEA | R Documentation |
This function makes use of Seurat::FindAllMarkers()
to compute
the differently expressed genes across the groups of
the grouping variable denoted in the argument across
.
See details for more.
runDEA(
object,
across,
method_de = NULL,
verbose = NULL,
base = 2,
variable.features.n = 3000,
...
)
runDeAnalysis(...)
object |
A valid spata-object. |
across |
Character value or NULL. Specifies the grouping variable of interest. Use |
method_de |
Character value. Denotes the method to according to which the de-analysis is performed.
Given to argument |
... |
Additional arguments given to |
fc_name , base |
Given to corresponding arguments of |
This function is a wrapper around the DEA pipeline from the Seurat
package. It creates a temporary Seurat
object via Seurat::CreateSeuratObject()
,
and Seurat::SCTransform()
. Then, Seurat::FindAllMarkers()
is run. The output data.frame
is stored in the SPATA2
object which is returned at the end.
If across
and/or method_de
are vectors instead of single
values runDEA()
iterates over all combinations in a for-loop and
stores the results in the respective slots. (e.g.: If across
= 'seurat_clusters'
and method_de
= c('wilcox', 'bimod') the function computes the differently expressed genes
across all groups found in the feature variable seurat_clusters according to method wilcox and
stores the results in the respective slot. Then it does the same according to method bimod.)
The results are obtainable via getDeaResults()
, getDeaResultsDf()
and getDeaGenes()
.
The input spata2
object containing the added or computed
results.
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