A function to perform DE analysis on CITE seq data

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)