GenesSpaceEmbedding: Gene Space Embedding

In soedinglab/merlot: MERLoT

Description

Embeds an elastic principal tree on the gene expression space from which the initial cell coordinates were calculated. The function receives the original Expression Matrix from which a lowe dimensional manifold was calculated and the coordinates from the low-dimensional manifold.

Usage

GenesSpaceEmbedding(ExpressionMatrix, ElasticTree, lambda_0 = 2.03e-09,
  mu_0 = 0.00625, increaseFactor_mu = 20, increaseFactor_lambda = 20,
  NCores = 1)

Arguments

ExpressionMatrix	Gene expression matrix on which the tree will be embedded
ElasticTree	elastic tree to be embedded on the gene expression space
lambda_0	principal elastic tree energy function parameter.
mu_0	principal elastic tree energy function parameter
increaseFactor_mu	factor by which the principal elastic tree energy function parameters will be increased for the embedding
increaseFactor_lambda	factor by which the principal elastic tree energy function parameters will be increased for the embedding
NCores	number of CPU cores to be used for the calculation

soedinglab/merlot documentation built on June 28, 2020, 9:36 a.m.