SelectGenesets: Select genesets for embedding

Description Usage Arguments Value

View source: R/annotate_nmf.R

Description

Select genesets for embedding

Usage

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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 Dec. 18, 2018, 2:39 a.m.