DEgenes: DEgenes

In SydneyBioX/CiteFuse: CiteFuse: multi-modal analysis of CITE-seq data

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)

SydneyBioX/CiteFuse documentation built on Feb. 13, 2023, 6:04 a.m.