SelectGenesets: Select genesets for embedding

In yanwu2014/swne: Similarity Weighted Nonnegative Embedding: A method for visualizing high dimensional datasets

Select genesets for embedding

Description

Select genesets for embedding

Usage

SelectGenesets(
  norm.counts,
  nmf.scores,
  genesets,
  assoc.metric = "pearson",
  method = "lm",
  n.cores = 8,
  genesets.return = 5
)

Arguments

norm.counts	Normalized input data
nmf.scores	NMF factors (factors x samples)
genesets	List of genesets to use
method	Method used to project data onto genesets. lm uses a simple linear model while mf will use a masked version of nmf.
n.cores	Number of cores to use
genesets.return	Number of genesets to return for each factor

Value

dataframe of top genesets associated with each factor

yanwu2014/swne documentation built on Aug. 5, 2023, 4:42 a.m.