get_cluster_markers: get_cluster_markers

In aertslab/SCopeLoomR: Build .loom files (compatible with SCope) and extract data from .loom files.

get_cluster_markers

Description

Get a list of data.frame each containing the statistical markers for the clusters from the clustering with the given clustering.name and filtered with the given log.fc.threshold and given adj.p.value.

Usage

get_cluster_markers(
  loom,
  clustering.id = NULL,
  clustering.name = NULL,
  log.fc.threshold = 1.5,
  adj.p.value.threshold = 0.05,
  n.signif.digits = NULL
)

Arguments

loom	The loom file handler.
clustering.name	The name/description of the clustering.
log.fc.threshold	The log fold change threshold
adj.p.value.threshold	The adjusted p-value threshold

Value

A list of L data.frame of N-by-M containing the statistical markers for all the clusters of from the clusteirng with the given clustering.name. L represents the number of clusters. N represents the number of statistical markers for a given cluster.

aertslab/SCopeLoomR documentation built on April 19, 2022, 11:25 a.m.