selectDEgenes {CiteFuse} | R Documentation

## selectDEgenes

### Description

A function to select DE genes

### Usage

    selectDEgenes(
      sce = NULL,
      de_res = NULL,
      altExp_name = "none",
      pval_adj = 0.05,
      mean_diff = 0,
      pct_diff = 0.1,
      topN = 10
    )

### Arguments

`sce` | A SingleCellExperiment object with DE results stored in meta data DE_res list.
`de_res` | DE_res returned by DEgenesCross().
`altExp_name` | A character indicates which expression matrix is used. by default is none (i.e. RNA).
`pval_adj` | A numeric indicates the threshold of adjusted p-value.
`mean_diff` | A numeric indicates the threshold of difference of average expression.
`pct_diff` | A numeric indicates the threshold of difference of percentage expression.
`topN` | A numeric indicates the top number of genes will be included in the list.

### Value

A SingleCellExperiment With filtered DE results in DE_res_filter list of metadata

### Examples

    data(sce_control_subset)
    sce_control_subset <- DEgenes(sce_control_subset,
    group = sce_control_subset$SNF_W_louvain,
    return_all = TRUE,
    exprs_pct = 0.5)

    sce_control_subset <- selectDEgenes(sce_control_subset)

[Package CiteFuse version 1.0.0 Index]