DEgenes {CiteFuse} | R Documentation

## DEgenes

### Description

A function to perform DE analysis on CITE seq data

### Usage

    DEgenes(
      sce,
      altExp_name = "none",
      exprs_value = "logcounts",
      group = NULL,
      method = "wilcox",
      exprs_pct = 0.1,
      exprs_threshold = 0,
      return_all = FALSE,
      pval_adj = 0.05,
      mean_diff = 0,
      pct_diff = 0.1,
      topN = 10
    )

### Arguments

`sce` | A SingleCellExperiment object
`altExp_name` | A character indicates which expression matrix is used. by default is none (i.e. RNA).
`exprs_value` | A character indicates which expression value in assayNames is used.
`group` | A vector indicates the grouping of the data
`method` | A character indicates the method used in DE analysis
`exprs_pct` | A numeric indicates the threshold expression percentage of a gene to be considered in DE analysis
`exprs_threshold` | A numeric indicates the threshold of expression. By default is 0.
`return_all` | Whether return full list of DE genes
`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 SingleCellExeperiment with DE results stored in meta data DE_res

### 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]