EmbedPromoters: Embeds genes based on promoter accessibility relative to...

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

Embeds genes based on promoter accessibility relative to topic coordinates

Description

Embeds genes based on promoter accessibility relative to topic coordinates

Usage

EmbedPromoters(
  swne.embedding,
  cisTopicObject,
  genes.embed,
  peaks.use = NULL,
  alpha.exp = 1,
  n_pull = 3,
  scale.cols = T,
  overwrite = T,
  promoterOnly = T
)

Arguments

swne.embedding	SWNE embedding computed using RunSWNE
cisTopicObject	cisTopic object
genes.embed	Genes to embed
peaks.use	Subset of peaks to use
alpha.exp	Increasing alpha.exp increases how much the factors "pull" the features
n_pull	Number of factors pulling on each feature. Must be >= 3
scale.cols	Whether or not to scale the input columns to 0 - 1
overwrite	Whether or not to overwrite any existing feature embedding
promoterOnly	Whether or not to only use promoter accessibility, otherwise the accessibility of the entire gene body will be used

Value

swne.embedding with feature coordinates (feature.coords)

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