runTsne: runTsne

In martinenge/RNAseqFunctions: RNA sequencing functions for the Enge lab

Description

This method runs t-SNE based on an input of 1-Pearson's correlation. Uses the Rtsne function from the Rtsne package.

Usage

runTsne(my.dist, dims = 2, theta = 0, initial_dims = 50,
  max_iter = 2000, perplexity = 10, seed = 11, is_distance = TRUE,
  ...)

Arguments

my.dist	dist; Typically produced with the pearsonsCor function.
dims	integer; Argument to Rtsne. Output dimensionality (default: 2)
theta	numeric; Argument to Rtsne. Speed/accuracy trade-off (increase for less accuracy), set to 0.0 for exact TSNE (default: 0)
initial_dims	integer; Argument to Rtsne. The number of dimensions that should be retained in the initial PCA step (default: 50)
max_iter	integer; Argument to Rtsne. Number of iterations (default: 2000)
perplexity	numeric; Argument to Rtsne. Perplexity parameter (should not be bigger than 3 * perplexity < nrow(X) - 1). (default = 10)
seed	The desired seed to set before running.
is_distance	logical; Argument to Rtsne. Indicate whether X is a distance matrix (default = TRUE).
...	Additional arguments to pass on

Value

Matrix containing the new representations for the objects.

Author(s)

Jason T. Serviss

Examples

pc <- pearsonsCor(testingCounts[, -1])
t <- runTsne(pc, perplexity = 2)

martinenge/RNAseqFunctions documentation built on May 28, 2019, 3:10 p.m.