get_eigen: Compute module eigen genes

Description Usage Arguments Details Value

View source: R/reduceDimension_WGCNA.R

Description

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Usage

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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.

Details

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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 Nov. 6, 2018, 9:47 p.m.