geneCluster: Gene clustering based on allelic ratio matrix with...

In Wancen/airpart: Differential cell-type-specific allelic imbalance

Gene clustering based on allelic ratio matrix with pseudo-count

Description

Gene clustering based on allelic ratio matrix with pseudo-count

Usage

geneCluster(
  sce,
  G,
  method = c("GMM", "hierarchical"),
  minClusterSize = 3,
  plot = TRUE,
  ...
)

Arguments

sce	SingleCellExperiment containing assays "ratio_pseudo" and colData factor "x"
G	An integer vector specifying the numbers of clusters for which the BIC is to be calculated. The default is G=c(8, 12, 16, 20, 24).
method	the method to do gene clustering. The default is the Gaussian Mixture Modeling which is likely to be more accurate. "hierarchical" represents automatic hierarchical clustering which is faster to compute.
minClusterSize	Minimum cluster size of "hierarchical" method.
plot	logical, whether to make a PCA plot
...	Catches unused arguments in indirect or list calls via do.call as described in Mclust

Value

gene cluster IDs are stored in the rowData column cluster and a table of gene cluster is returned in metadata geneCluster

References

This function leverages Mclust from the mclust package, or hclust.

For mclust see: Luca Scrucca and Michael Fop and T. Brendan Murphy, Adrian E. Raftery "mclust 5: clustering, classification and density estimation using Gaussian finite mixture models" 2016. The R Journal. doi: 10.32614/RJ-2016-021

See Also

Mclust

Examples

sce <- makeSimulatedData()
sce <- preprocess(sce)
sce <- geneCluster(sce, G = seq_len(4))

Wancen/airpart documentation built on March 12, 2023, 11:53 a.m.