get.variable.genes: Identify Highly Variable Genes

In robustSingleCell: Robust Clustering of Single Cell RNA-Seq Data

Description

Get highly variable genes by Heteroscedasticity controlled binning of gene expression measurements within each dataset separately.

Usage

get.variable.genes(environment, min.mean = 0.05, min.frac.cells = 0,
  min.dispersion.scaled = 1, rerun = F)

Arguments

environment	environment object
min.mean	minimum mean expression per gene
min.frac.cells	minimum fraction of cells expressing each gene
min.dispersion.scaled	minimum dispersion value
rerun	whether to rerun the analysis or load from cache

Value

environment parameter containing highly variable genes selection

Examples

LCMV1 <- setup_LCMV_example()
LCMV1 <- get.variable.genes(LCMV1)

Example output

Registered S3 method overwritten by 'GGally':
  method from   
  +.gg   ggplot2
[1] 1504   49
Computing
Time difference of 0.1290169 secs

Computing

robustSingleCell documentation built on May 2, 2019, 2:11 p.m.