ProjectGenesets: Projects dataset onto genesets using either NMF or a...

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

Projects dataset onto genesets using either NMF or a nonnegative linear model

Description

Projects dataset onto genesets using either NMF or a nonnegative linear model

Usage

ProjectGenesets(
  norm.counts,
  genesets,
  method = "lm",
  loss = "mse",
  n.cores = 1
)

Arguments

norm.counts	Normalized input data
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.
loss	Loss function for the nonnegative linear model
n.cores	Number of cores to use

Value

List of gene loadings and factor scores, with each factor corresponding to a geneset

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