selectDEgenes: selectDEgenes

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

selectDEgenes

Description

A function to select DE genes

Usage

selectDEgenes(
  sce = NULL,
  de_res = NULL,
  altExp_name = "none",
  pval_adj = 0.05,
  mean_diff = 0,
  pct_diff = 0.1,
  topN = 10
)

Arguments

sce	A SingleCellExperiment object with DE results stored in meta data DE_res list.
de_res	DE_res returned by DEgenesCross().
altExp_name	A character indicates which expression matrix is used. by default is none (i.e. RNA).
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 SingleCellExperiment With filtered DE results in DE_res_filter list of metadata

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.