differential_ChromSCape: Differential analysis with ChromSCape (differential...

In vallotlab/IDclust: Iterative Differential Clustering for single-cell

Differential analysis with ChromSCape (differential activation)

Description

Runs ChromSCape::differential_activation() function on clusters in the 'by' column of the SingleCellExperiment object and returns a data.frame containing the differential features that passed the thresholds.

Usage

differential_ChromSCape(
  object,
  by = "IDcluster",
  logFC.th = log2(2),
  qval.th = 0.01,
  min.pct = 0.2,
  marker = c("pos", "neg", "diff")[1]
)

Arguments

object	A SingleCellExperiment object containing scRNA dataset with a metadata column name matching the by parameter
by	A character specifying the name of the metadata column referencing the clusters.
logFC.th	A positive numeric specifying the log2 fold change of activation above/below which a feature is considered as significantly differential.
qval.th	A numeric specifying the adjusted p-value below which a feature is considered as significantly differential.
min.pct	Minimum percentage of cells to be active in the cells of the cluster to consider a feature as potentially significantly differential.
marker	A character specifying which markers to retrieve. 'pos' for positive markers (default), 'neg' for negative markers or 'diff' for differential markers.

See Also

See ChromSCape::differential_activation()

Examples

if(requireNamespace("ChromSCape", quietly=TRUE)){
 data("scExp", package = "IDclust")
DA <- differential_ChromSCape(scExp)
}

vallotlab/IDclust documentation built on Feb. 16, 2023, 8:58 a.m.