getStableClusters: Iterative merging of clusters along tree until stable

In JEFworks/MUDAN: Multi-sample Unified Discriminant ANalysis

Description

Iterative merging of clusters along tree until stable

Usage

getStableClusters(cd, com, matnorm, z.threshold = 3,
  hclust.method = "ward.D", min.group.size = 10, min.diff.genes = nrow(cd)
  * 0.005, max.iter = 10, removeGenes = "^RP|^MT", verbose = TRUE,
  plot = FALSE)

Arguments

cd	Counts matrix for differential expression analysis. Rows are genes. Columns are cells.
com	Community/group annotations for cells
matnorm	Normalized gene expression matrix for building group relationship tree. Rows are genes. Columns are cells.
z.threshold	Z-score threshold for identifying significantly differentially expressed genes
hclust.method	Hierarchical clustering method used to construct relationship tree
min.group.size	Minimum group size for stable cluster
min.diff.genes	Minimum number of significantly differentially expressed genes that must be identified or else groups will be merged
max.iter	Maximum number of iterations. Will end earlier if convergence reached.
removeGenes	Regex expression matching genes you want to remove such as ribosomal or mitochondrial genes.
verbose	Verbosity
plot	Whether to plot intermediate plots (hierarchical clustering dendrograms)

JEFworks/MUDAN documentation built on June 19, 2021, 6:46 a.m.