variableGenes: Identify a highly variable gene set

In MetaNeighbor: Single cell replicability analysis

Description

Identifies genes with high variance compared to their median expression (top quartile) within each experimentCertain function

Usage

variableGenes(
  dat,
  i = 1,
  exp_labels,
  min_recurrence = length(unique(exp_labels)),
  downsampling_size = 10000
)

Arguments

dat	SummarizedExperiment object containing gene-by-sample expression matrix.
i	default value 1; non-zero index value of assay containing the matrix data
exp_labels	character vector that denotes the source (Study ID) of each sample.
min_recurrence	Number of studies across which a gene must be detected as highly variable to be kept. By default, only genes that are variable across all studies are kept (intersection).
downsampling_size	Downsample each study to downsampling_size samples without replacement. If set to 0 or value exceeds dataset size, no downsampling is applied.

Value

The output is a vector of gene names that are highly variable in every experiment (intersect)

Examples

data(mn_data)
var_genes = variableGenes(dat = mn_data, exp_labels = mn_data$study_id)
var_genes

MetaNeighbor documentation built on Nov. 8, 2020, 5:40 p.m.