tSNE {scGPS} | R Documentation

## tSNE

### Description

calculate tSNE from top variable genes

### Usage

    tSNE(
      expression.mat = NULL,
      topgenes = 1500,
      scale = TRUE,
      thet = 0.5,
      perp = 30
    )

### Arguments

`expression.mat` | An expression matrix, with genes in rows
`topgenes` | number of genes used for clustering calculations.
`scale` | a logical of whether we want to scale the matrix
`thet` | numeric; Speed/accuracy trade-off (increase for less accuracy)
`perp` | numeric; Perplexity parameter (should not be bigger than 3 * perplexity < nrow(X) - 1, see details for interpretation)

### Value

a tSNE reduced matrix containing three tSNE dimensions

### Examples

    day2 <- day_2_cardio_cell_sample
    mixedpop1 <-new_scGPS_object(ExpressionMatrix = day2$dat2_counts,
        GeneMetadata = day2$dat2geneInfo, CellMetadata = day2$dat2_clusters)
    t <-tSNE(expression.mat = assay(mixedpop1))

[Package scGPS version 1.8.0 Index]