RunCCA | R Documentation |
Runs a canonical correlation analysis using a diagonal implementation of CCA.
For details about stored CCA calculation parameters, see
PrintCCAParams
.
RunCCA(object1, object2, ...)
## Default S3 method:
RunCCA(
object1,
object2,
standardize = TRUE,
num.cc = 20,
seed.use = 42,
verbose = FALSE,
...
)
## S3 method for class 'Seurat'
RunCCA(
object1,
object2,
assay1 = NULL,
assay2 = NULL,
num.cc = 20,
features = NULL,
renormalize = FALSE,
rescale = FALSE,
compute.gene.loadings = TRUE,
add.cell.id1 = NULL,
add.cell.id2 = NULL,
verbose = TRUE,
...
)
object1 |
First Seurat object |
object2 |
Second Seurat object. |
... |
Extra parameters (passed onto MergeSeurat in case with two objects passed, passed onto ScaleData in case with single object and rescale.groups set to TRUE) |
standardize |
Standardize matrices - scales columns to have unit variance and mean 0 |
num.cc |
Number of canonical vectors to calculate |
seed.use |
Random seed to set. If NULL, does not set a seed |
verbose |
Show progress messages |
assay1 , assay2 |
Assays to pull from in the first and second objects, respectively |
features |
Set of genes to use in CCA. Default is the union of both the variable features sets present in both objects. |
renormalize |
Renormalize raw data after merging the objects. If FALSE, merge the data matrices also. |
rescale |
Rescale the datasets prior to CCA. If FALSE, uses existing data in the scale data slots. |
compute.gene.loadings |
Also compute the gene loadings. NOTE - this will scale every gene in the dataset which may impose a high memory cost. |
add.cell.id1 , add.cell.id2 |
Add ... |
Returns a combined Seurat object with the CCA results stored.
merge.Seurat
## Not run:
data("pbmc_small")
pbmc_small
# As CCA requires two datasets, we will split our test object into two just for this example
pbmc1 <- subset(pbmc_small, cells = colnames(pbmc_small)[1:40])
pbmc2 <- subset(pbmc_small, cells = colnames(x = pbmc_small)[41:80])
pbmc1[["group"]] <- "group1"
pbmc2[["group"]] <- "group2"
pbmc_cca <- RunCCA(object1 = pbmc1, object2 = pbmc2)
# Print results
print(x = pbmc_cca[["cca"]])
## End(Not run)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.