variableGenes {MetaNeighbor} | R Documentation

## Identify a highly variable gene set

### 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

[Package MetaNeighbor version 1.14.0 Index]