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

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"))