Description Usage Arguments Value Examples
Creates a Seurat object containing only a subset of the cells in the original object. Takes either a list of cells to use as a subset, or a parameter (for example, a gene), to subset on.
1 2 3 4 5 6 7 8 9 10 11 12 | SubsetData(object, ...)
## S3 method for class 'Assay'
SubsetData(object, cells = NULL, subset.name = NULL,
low.threshold = -Inf, high.threshold = Inf, accept.value = NULL,
...)
## S3 method for class 'Seurat'
SubsetData(object, assay = NULL, cells = NULL,
subset.name = NULL, ident.use = NULL, ident.remove = NULL,
low.threshold = -Inf, high.threshold = Inf, accept.value = NULL,
max.cells.per.ident = Inf, random.seed = 1, ...)
|
object |
An object |
... |
Arguments passed to other methods |
cells |
A vector of cell names to use as a subset. If NULL (default), then this list will be computed based on the next three arguments. Otherwise, will return an object consissting only of these cells |
subset.name |
Parameter to subset on. Eg, the name of a gene, PC1, a column name in object@meta.data, etc. Any argument that can be retreived using FetchData |
low.threshold |
Low cutoff for the parameter (default is -Inf) |
high.threshold |
High cutoff for the parameter (default is Inf) |
accept.value |
Returns cells with the subset name equal to this value |
assay |
Assay to subset on |
ident.use |
Create a cell subset based on the provided identity classes |
ident.remove |
Subtract out cells from these identity classes (used for filtration) |
max.cells.per.ident |
Can be used to downsample the data to a certain max per cell ident. Default is INF. |
random.seed |
Random seed for downsampling |
Returns a Seurat object containing only the relevant subset of cells
1 2 | pbmc1 <- SubsetData(object = pbmc_small, cells = colnames(x = pbmc_small)[1:40])
pbmc1
|
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