Description Usage Arguments Value
This function prepares an object of SingleCellExperiment
class for SC3
clustering. It
creates and populates the following items of the sc3
slot of the metadata(object)
:
kmeans_iter_max
 the same as the kmeans_iter_max
argument.
kmeans_nstart
 the same as the kmeans_nstart
argument.
n_dim
 contains numbers of the number of eigenvectors to be used
in kmeans
clustering.
rand_seed
 the same as the rand_seed
argument.
svm_train_inds
 if SVM is used this item contains indexes of the
training cells to be used for SC3 clustering and further SVM prediction.
svm_study_inds
 if SVM is used this item contains indexes of the
cells to be predicted by SVM.
n_cores
 the same as the n_cores
argument.
1 2 3 4 5 6 7 8 9 10  sc3_prepare.SingleCellExperiment(object, gene_filter, pct_dropout_min,
pct_dropout_max, d_region_min, d_region_max, svm_num_cells, svm_train_inds,
svm_max, n_cores, kmeans_nstart, kmeans_iter_max, rand_seed)
## S4 method for signature 'SingleCellExperiment'
sc3_prepare(object, gene_filter = TRUE,
pct_dropout_min = 10, pct_dropout_max = 90, d_region_min = 0.04,
d_region_max = 0.07, svm_num_cells = NULL, svm_train_inds = NULL,
svm_max = 5000, n_cores = NULL, kmeans_nstart = NULL,
kmeans_iter_max = 1e+09, rand_seed = 1)

object 
an object of 
gene_filter 
a boolen variable which defines whether to perform gene filtering before SC3 clustering. 
pct_dropout_min 
if 
pct_dropout_max 
if 
d_region_min 
defines the minimum number of eigenvectors used for
kmeans clustering as a fraction of the total number of cells. Default is 
d_region_max 
defines the maximum number of eigenvectors used for
kmeans clustering as a fraction of the total number of cells. Default is 
svm_num_cells 
number of randomly selected training cells to be used
for SVM prediction. The default is 
svm_train_inds 
a numeric vector defining indeces of training cells
that should be used for SVM training. The default is 
svm_max 
define the maximum number of cells below which SVM is not run. 
n_cores 
defines the number of cores to be used on the user's machine. If not set, 'SC3' will use all but one cores of your machine. 
kmeans_nstart 
nstart parameter passed to 
kmeans_iter_max 
iter.max parameter passed to 
rand_seed 
sets the seed of the random number generator. 
an object of SingleCellExperiment
class
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