ModuleHub: Enhanced hub genes exploration after FastWGCNA pipeline

In shijianasdf/BasicBioinformaticsAnalysisFromZhongShan: Launch Usual Clinical tool for Kind Yield

Description

The speed of ModuleHub is very fast.If you want to set different parameters(always hub_WeightedQ and cutoff.pval) for hub genes exploration, ModuleHub is a nice function to do it.

Usage

ModuleHub(object, design, variable, corType = "pearson",
  cutoff.pval = 1, hub_cutoffSigGM = 0.2, hub_MM = 0.8,
  hub_WeightedQ = 1, save.path = "WGCNA", names = "love")

Arguments

object	the result of FastWGCNA.
design	a trait-design object
variable	the variables you want to show in Module-Trait relationships plot.
corType	one of "pearson" and "bicor".Default is pearson
cutoff.pval	cut-off of the p value in significant module-phenotype filter
hub_cutoffSigGM	the cut-off of significant genes-Modules in hub genes exploration.Default is 0.2
hub_MM	the cut-off of Module Memberships in hub genes exploration.Default is 0.8
hub_WeightedQ	the cut-off of weighted q value in hub genes exploration.Default is 0.01
save.path	the space of the save file.Default is "WGCNA"
names	part of saved files name

Details

1.Only work on wgcna result with ONE Block. 2.cutoff.pval is a useful parameter.If you want significant module,you can set cutoff.pval = 0.05(or 0.01,It depends on your custom);If you want to see all the modules regardless of significance,just set cutoff.pval = 1. 3.hub_WeightedQ is a stricter filter for hub genes.If your hub genes is too much,you can set hub_WeightedQ = 0.05(or 0.01,It depends on your custom).However,most researchers do not use hub_WeightedQ to filter their hub genes and often use only hub_MM=0.8 and hub_cutoffSigGM=0.2.

Value

LuckWGCNA object

Author(s)

Weibin Huang<[e-mail]>

See Also

FastWGCNA.

Examples

## This is a simulative process and available only with CORRECT VARIABLES
library(lucky)
load("E:/RCloud/RFactory/lucky/love/WGCNA-test/love_wgcna.rda")
object = wgcna;rm(wgcna);gc()
design = rna.design.tumor
variable = c("age","his1","gender","N.status","T.status")
result_MH <- ModuleHub(object,
                       design,
                       variable,
                       save.path = "WGCNA",
                       names = "love")

shijianasdf/BasicBioinformaticsAnalysisFromZhongShan documentation built on Jan. 3, 2020, 10:08 p.m.