PerformIntegration | R Documentation |
This perform's Seurat's integration on a dataset
PerformIntegration(
seuratObj,
splitField = "SubjectId",
nVariableFeatures = 4000,
nIntegrationFeatures = 3500,
k.weight = 20,
dimsToUse = 20,
integrationFeaturesInclusionList = NULL,
integrationFeaturesExclusionList = NULL,
minCellsPerSubsetObject = 75,
dropGroupsBelowThreshold = TRUE
)
seuratObj |
A Seurat object. |
splitField |
The metadata field on which to split the seurat object for integration |
nVariableFeatures |
The number of variable features used for Seurat::FindVariableFeatures |
nIntegrationFeatures |
The number of features for Seurat::SelectIntegrationFeatures |
k.weight |
Passed to Seurat::IntegrateData() |
dimsToUse |
Passed to Seurat::IntegrateData(), as dims = 1:dimsToUse |
integrationFeaturesInclusionList |
An optional vector of genes that will be included in the integration genes |
integrationFeaturesExclusionList |
An optional vector of genes that will be excluded in the integration genes |
minCellsPerSubsetObject |
If any of the seurat objects after splitting on splitField have fewer than this many cells, they are either discarded or the function will throw an error, depending on dropGroupsBelowThreshold |
dropGroupsBelowThreshold |
If any of the seurat objects after splitting are below minCellsPerSubsetObject and if this param is true, they will be discarded. |
A modified Seurat object.
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