View source: R/fct_09_network.R
get_wgcna | R Documentation |
Run the WGCNA package on the processed data.
get_wgcna(data, n_genes, soft_power, min_module_size)
data |
Data matrix that has been through the pre-processing |
n_genes |
Number of most variable genes to use in the function |
soft_power |
Value between 1-20 (https://support.bioconductor.org/p/87024/) |
min_module_size |
For modules detected by WGCNA, set a minimum size |
A list of 8 objects. data
is a submatrix of the input
parameter data
which on contains the genes that were selected with
n_genes
. powers
is a numeric vector from 1-10 and then the
even numbers from 10-20. sft
is a return from the WGCNA package that
is a list containing powerEstimate
and fitIndices
. For
information on these objects visit
https://www.rdocumentation.org/packages/WGCNA/versions/1.70-3/topics/pickSoftThreshold.
tom
is another return from the WGCNA package, for information on this
matrix visit https://www.rdocumentation.org/packages/WGCNA/versions/1.70-3/topics/TOMsimilarityFromExpr.
dynamic_colors
is a vector of colors created by the WGCNA package to
correspond to the modules that were identified by the pacakage.
module_info
is a data frame with a gene name, a color, and the
identified module for the gene. n_modules
gives the number of modules
calculated. n_genes
tells the number of genes included in the
modules.
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