CORE_subcluster: sub_clustering (optional) after running CORE 'test'

In IMB-Computational-Genomics-Lab/scGPS: A complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)

Description

CORE_subcluster allows re-cluster the CORE clustering result

Usage

CORE_subcluster(
  mixedpop = NULL,
  windows = seq(from = 0.025, to = 1, by = 0.025),
  select_cell_index = NULL,
  ngenes = 1500
)

Arguments

mixedpop	is a SingleCellExperiment object from the train mixed population
windows	a numeric specifying the number of windows to test
select_cell_index	a vector containing indexes for cells in selected clusters to be reclustered
ngenes	number of genes used for clustering calculations.

Value

a list with clustering results of all iterations, and a selected optimal resolution

Author(s)

Quan Nguyen, 2017-11-25

Examples

day5 <- day_5_cardio_cell_sample
mixedpop2 <-new_summarized_scGPS_object(ExpressionMatrix = day5$dat5_counts,
    GeneMetadata = day5$dat5geneInfo, CellMetadata = day5$dat5_clusters)
test <- CORE_clustering(mixedpop2,remove_outlier= c(0))

IMB-Computational-Genomics-Lab/scGPS documentation built on Dec. 6, 2020, 3:20 p.m.