sub_clustering {scGPS}R Documentation

sub_clustering for selected cells

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)))

[Package scGPS version 1.4.0 Index]