sub_clustering: sub_clustering for selected cells

In scGPS: A complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)

Description

performs 40 clustering runs or more depending on windows

Usage

sub_clustering(object = NULL, ngenes = 1500, windows = seq(from =
  0.025, to = 1, by = 0.025), select_cell_index = NULL)

Arguments

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

Value

clustering results

Author(s)

Quan Nguyen, 2018-01-31

Examples

day5 <- day_5_cardio_cell_sample
mixedpop2 <-new_summarized_scGPS_object(ExpressionMatrix = day5$dat5_counts, 
    GeneMetadata = day5$dat5geneInfo, CellMetadata = day5$dat5_clusters)
test_sub_clustering <-sub_clustering(mixedpop2,
    select_cell_index = c(seq_len(100)))

scGPS documentation built on Nov. 8, 2020, 5:22 p.m.