selectGenes: Select highly variable genes

In lingxuez/SOUP: Semi-soft Clustering of Single Cell Data

Description

Select highly variable genes for SOUP clustering, using SPCA and/or DESCEND.

Usage

selectGenes(expr, type = "count", SPCA = TRUE, DESCEND = TRUE,
  n.cores = 1, threshold = 3, sumabs = 0.05, nPC = 3)

Arguments

expr	a cell-by-gene expression matrix, either the raw counts or log-transformed expressions.
type	"count" if expr contains the raw counts (default), or "log" if expr has been normalized and log-transformed.
SPCA	boolean, whether to use SPCA or not.
DESCEND	boolean, whether to use DESCEND or not.
n.cores	the number of cores used for parallel computing of DESCEND. DESCEND can be slow so parallelization is highly recommended.
threshold	the threshold for Gini index of DESCEND. Higer threshold leads to fewer selected genes.
sumabs	a measurement of sparsity of genes in SPCA, between 1/sqrt(n.gene) and 1. Smaller values result in sparser results, hence fewer selected genes.
nPC	the number of sparse singular vectors to use in SPCA.

Value

A list of gene names that are selected.

lingxuez/SOUP documentation built on May 28, 2019, 3:38 p.m.