sc3: Run all steps of 'SC3' in one go

Description Usage Arguments Value

Description

This function is a wrapper that executes all steps of SC3 analysis in one go.

Usage

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sc3.SingleCellExperiment(object, ks, 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, k_estimator, biology,
  rand_seed)

## S4 method for signature 'SingleCellExperiment'
sc3(object, ks = NULL, 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, k_estimator = FALSE, biology = FALSE,
  rand_seed = 1)

Arguments

object

an object of SingleCellExperiment class.

ks

a range of the number of clusters k used for SC3 clustering. Can also be a single integer.

gene_filter

a boolen variable which defines whether to perform gene filtering before SC3 clustering.

pct_dropout_min

if gene_filter = TRUE, then genes with percent of dropouts smaller than pct_dropout_min are filtered out before clustering.

pct_dropout_max

if gene_filter = TRUE, then genes with percent of dropouts larger than pct_dropout_max are filtered out before clustering.

d_region_min

defines the minimum number of eigenvectors used for kmeans clustering as a fraction of the total number of cells. Default is 0.04. See SC3 paper for more details.

d_region_max

defines the maximum number of eigenvectors used for kmeans clustering as a fraction of the total number of cells. Default is 0.07. See SC3 paper for more details.

svm_num_cells

number of randomly selected training cells to be used for SVM prediction. The default is NULL.

svm_train_inds

a numeric vector defining indeces of training cells that should be used for SVM training. The default is NULL.

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 function. Can be set manually. By default it is 1000 for up to 2000 cells and 50 for more than 2000 cells.

kmeans_iter_max

iter.max parameter passed to kmeans function.

k_estimator

boolean parameter, defines whether to estimate an optimal number of clusters k. If user has already defined the ks parameter the estimation does not affect the user's paramater.

biology

boolean parameter, defines whether to compute differentially expressed genes, marker genes and cell outliers.

rand_seed

sets the seed of the random number generator. SC3 is a stochastic method, so setting the rand_seed to a fixed values can be used for reproducibility purposes.

Value

an object of SingleCellExperiment class


hemberg-lab/SC3 documentation built on May 11, 2018, 4:32 p.m.