robustSingleCell (version 0.1.1)

get.robust.markers: Get Robust Marker

Description

Analysis of robust subpopulation marker prioritization

Usage

get.robust.markers(environment, cluster_group1, cluster_group2,
  group1_label, group2_label, annotate.genes = NA, min.fold.diff = 1.5,
  min.ratio.diff = 3, QValue = 0.05)

Arguments

environment

environment object

cluster_group1

cluster group 1 to be used as a foreground

cluster_group2

cluster group 2 to be used as a background

group1_label

label for group 1

group2_label

label for group 2

annotate.genes

specific gene names to annotate in figure in addition to novel markers

min.fold.diff

average expression fold change cutoff

min.ratio.diff

detection ratio fold change cutoff

QValue

Qvalue cutoff

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)
diff_exp <- get.robust.markers(LCMV1,
cluster_group1 = c('1','2'),
cluster_group2 = c('3','4'),
group1_label = 'CD4 T Cells',
group2_label = 'CD8 T Cells')
# }