get.robust.markers: Get Robust Marker

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

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

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')

robustSingleCell documentation built on May 2, 2019, 2:11 p.m.