get_eigen: Compute module eigen genes

In AllenInstitute/scrattch.hicat: Hierarchical Iterative Clustering Analysis for Transcriptomic data

Compute module eigen genes

Description

Compute module eigen genes

Usage

get_eigen(
  gene.mod,
  norm.dat,
  select.cells = colnames(norm.dat),
  prefix = NULL,
  method = "ward.D",
  hc = NULL,
  ...
)

Arguments

gene.mod	A list of gene modules.
norm.dat	log transformed normalized data matrix.
select.cells	Cells used to compute module eigen genes.
prefix	Default NULL. If not NULL, a heatmap of the gene module eigen genes will be produced with "prefix" as the prefix for the pdf file.
method	Default "ward.D". Used by hclust method to create the cell dendrogram for the heatmap display.
hc	Precomputed cell dendrogram for heatmap display. Default NULL.
...	Other plotting parameters passed to the heatmap function.

Value

A list with two elements: module eigen genes, and if prefix is not NULL, dendrogram for selected cells.

AllenInstitute/scrattch.hicat documentation built on June 6, 2024, 5:31 a.m.