runClusterSummaryMetrics: Run Cluster Summary Metrics

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Run Cluster Summary Metrics

Description

Calculates the mean expression of percent of cells that express the given genes for each cluster

Usage

runClusterSummaryMetrics(
  inSCE,
  useAssay = "logcounts",
  featureNames,
  displayName = NULL,
  groupNames = "cluster",
  scale = FALSE
)

Arguments

inSCE	The single cell experiment to use.
useAssay	The assay to use.
featureNames	A string or vector of strings with each gene to aggregate.
displayName	A string that is the name of the column used for genes.
groupNames	The name of a colData entry that can be used as groupNames.
scale	Option to scale the data. Default: /codeFALSE. Selected assay will not be scaled.

Value

A dataframe with mean expression and percent of cells in cluster that express for each cluster.

Examples

data("scExample")
runClusterSummaryMetrics(inSCE=sce, useAssay="counts", featureNames=c("B2M", "MALAT1"), 
displayName="feature_name", groupNames="type")

compbiomed/singleCellTK documentation built on Feb. 10, 2024, 3:32 a.m.