get_all_cluster_markers: get_all_cluster_markers

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

get_all_cluster_markers

Description

Get cluster markers from all clusterings fromthe given loom file with filter applied by the given log.fc.threshold and adj.p.value.threshold.

Usage

get_all_cluster_markers(
  loom,
  log.fc.threshold = 1.5,
  adj.p.value = 0.05,
  n.signif.digits = NULL
)

Arguments

loom	The loom file handler.
log.fc.threshold	The log fold change threshold
n.signif.digits	Number of significant digits in the output.
adj.p.value.threshold	The adjusted p-value threshold

Value

A list of data.frames containing all the clusterings with their cluster markers (adj. p-value and log fold changes). The list names refer to the different clustering names.

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