robustSingleCell (version 0.1.1)

get.cluster.names: 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

# NOT RUN {
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)
# }