PseudobulkSeurat | R Documentation |
Aggregates raw counts in the seurat object, generating a new seurat object where each same has the sum of the counts, grouped by the desired variables
PseudobulkSeurat(
seuratObj,
groupFields,
assayToAggregate = Seurat::DefaultAssay(seuratObj),
additionalFieldsToAggregate = NULL,
metaFieldCollapseCharacter = "|",
nCountRnaStratification = F,
stratificationGroupingFields = c("ClusterNames_0.2", "ClusterNames_0.4",
"ClusterNames_0.6", "ClusterNames_0.8", "ClusterNames_1.2")
)
seuratObj |
The seurat object |
groupFields |
The set of fields on which to group |
assayToAggregate |
The assay to aggregate |
additionalFieldsToAggregate |
An option list of additional fields (which must be numeric). Per field, the mean per group will be computed and stored in the output object. |
metaFieldCollapseCharacter |
The character to use when concatenating metadata fields together to form the sample key field |
nCountRnaStratification |
A boolean determining whether or not automatic outlier detection of clusters with abnormal nCount_RNA should be detected. |
stratificationGroupingFields |
The metadata fields containing groupings of cells to be specified as having abnormal nCount_RNA distributions or not. The "leftmost"/first argument that detects an outlier will break the looping and sequester cells at that value. It is recommended that this vector is arranged by a "least to most" specific hierarchy/progression. |
An aggregated Seurat object.
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