get.cluster.names: Get/Set Cluster Names by Marker Gene Expression

In asmagen/robustSingleCell: Robust Clustering of Single Cell RNA-Seq Data

Get/Set Cluster Names by Marker Gene Expression

Description

get.cluster.names uses predefined marker genes to assign clusters with putative cell type or state labels.

set.cluster.names saves the cluster names in storage and in the environment object

Usage

get.cluster.names(environment, types, min.fold = 1.25, max.Qval = 0.1,
  print = T)

set.cluster.names(environment, names)

Arguments

environment	environment object
types	data frame associating cell type or state with marker genes
min.fold	minimum fold change to consider a marker as overexpressed
max.Qval	maximum FDR q value to consider a marker as overexpressed
print	whether to print output calculations
names	cluster names defined in get.cluster.names

Value

get.cluster.names returns a vector containing assigned cluster name labels

set.cluster.names returns an environment object coded with cluster names

Functions

• set.cluster.names: set annotations to clusters

Examples

LCMV1 <- setup_LCMV_example()
LCMV1 <- get.variable.genes(LCMV1, min.mean = 0.1, min.frac.cells = 0,
min.dispersion.scaled = 0.1)
LCMV1 <- PCA(LCMV1)
LCMV1 <- cluster.analysis(LCMV1)
types = rbind(
data.frame(type='Tfh',gene=c('Tcf7','Cxcr5','Bcl6')),
data.frame(type='Th1',gene=c('Cxcr6','Ifng','Tbx21')),
data.frame(type='Tcmp',gene=c('Ccr7','Bcl2','Tcf7')),
data.frame(type='Treg',gene=c('Foxp3','Il2ra')),
data.frame(type='Tmem',gene=c('Il7r','Ccr7')),
data.frame(type='CD8',gene=c('Cd8a')),
data.frame(type='CD4', gene = c("Cd4")),
data.frame(type='Cycle',gene=c('Mki67','Top2a','Birc5'))
)
summarize(LCMV1)
cluster_names <- get.cluster.names(LCMV1, types, min.fold = 1.0, max.Qval = 0.01)
LCMV1 <- set.cluster.names(LCMV1, names = cluster_names)

asmagen/robustSingleCell documentation built on July 30, 2023, 6:48 a.m.