getRDS | R Documentation |
perform dimesion reduction using PCA using the expression profiles of genes satisfied the following criteria: included in the "gene.use", had log2 expression variance greater than min.var, and expressed (>1) in at least "min.cells" number of cells.
getRDS(
object,
genes.use = NULL,
method = "pca",
num_dim = 2,
log.base = 2,
do.center = TRUE,
do.scale = FALSE,
use.cor = T,
min.var = 0.5,
min.cells = 3,
...
)
object |
slice object |
genes.use |
The set of genes whose expression will be used for dimension reduction; if NULL, set to all genes |
method |
The method for dimension reduction; currently, only support "pca"; more options will be integrated soon |
num_dim |
The number of dimensions to be extracted |
log.base |
The base of logarithm |
do.center |
If TRUE, substract row-mean from each value |
do.scale |
If TRUE, divide by row standard deviation |
use.cor |
If TRUE, use Pearson's correlation matrix as input to prcomp function |
min.var |
The minimum expression variance for a gene to be included in dimension reduction |
min.cells |
The minimum number of expressed cells for a gene to be included in dimension reduction |
updated slice object with reduced dimensions in the "rds" slot, the first two components are also used to set the "vds" slot for visualization.
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