DEgenesCross

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"))