clustering {scGPS} | R Documentation |
performs 40 clustering runs or more depending on windows
clustering(object = NULL, ngenes = 1500, windows = seq(from = 0.025, to = 1, by = 0.025), remove_outlier = c(0), nRounds = 1, PCA = FALSE, nPCs = 20, verbose = FALSE)
object |
is a SingleCellExperiment object from the train mixed population |
ngenes |
number of top variable genes to be used |
windows |
a numeric specifying the number of windows to test |
remove_outlier |
a vector containing IDs for clusters to be removed the default vector contains 0, as 0 is the cluster with singletons |
nRounds |
number of iterations to remove a selected clusters |
PCA |
logical specifying if PCA is used before calculating distance matrix |
nPCs |
number of principal components from PCA dimensional reduction to be used |
verbose |
a logical whether to display additional messages |
clustering results
Quan Nguyen, 2017-11-25
day5 <- day_5_cardio_cell_sample mixedpop2 <-new_summarized_scGPS_object(ExpressionMatrix = day5$dat5_counts, GeneMetadata = day5$dat5geneInfo, CellMetadata = day5$dat5_clusters) test <-clustering(mixedpop2, remove_outlier = c(0))