DEgenesCross {CiteFuse} | R Documentation

## DEgenesCross

### Description

A function to perform DE analysis on a list of CITE seq data

### Usage

    DEgenesCross(
      sce_list,
      altExp_name = "none",
      exprs_value = "logcounts",
      method = "wilcox",
      colData_name = NULL,
      group_to_test = NULL,
      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_list` | A Slist of ingleCellExperiment 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.
`method` | A character indicates the method used in DE analysis
`colData_name` | A vector of character indicates the colData that stored the group information of each sce of the sce_list
`group_to_test` | A vector of character indicates which group in each sce is used to compared across the sce list.
`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", package = "CiteFuse")
    data("sce_ctcl_subset", package = "CiteFuse")

    de_res <- DEgenesCross(sce_list = list(control = sce_control_subset,
    ctcl = sce_ctcl_subset),
    colData_name = c("SNF_W_louvain", "SNF_W_louvain"),
    group_to_test = c("2", "6"))

[Package CiteFuse version 1.0.0 Index]