EmbedTFBS: Embeds genes based on TF binding site accessibility relative...

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

Embeds genes based on TF binding site accessibility relative to topic coordinates

Description

Embeds genes based on TF binding site accessibility relative to topic coordinates

Usage

EmbedTFBS(
  swne.embedding,
  cisTopicObject,
  motif_ix_mat = NULL,
  dev.mat = NULL,
  genes.embed,
  peaks.use = NULL,
  alpha.exp = 1,
  n_pull = 3,
  scale.cols = T,
  overwrite = T
)

Arguments

swne.embedding	SWNE embedding computed using RunSWNE
cisTopicObject	cisTopic object
motif_ix_mat	A binary matrix of peaks x TF motifs (can be generated with ChromVar)
dev.mat	A matrix of TF binding site accessibility generated from ChromVar
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

Value

swne.embedding with feature coordinates (feature.coords)

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