ModuleTraitValid: Get module-trait relationship given new validation cohorts

Description Usage Arguments Value Author(s) See Also Examples

View source: R/BI_ModuleTraitValid.R

Description

Get module-trait relationship given new validation cohorts. ModuleTraitValid supports multiple expression matrix.

Usage

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ModuleTraitValid(object, valid.matrix, log.convert = T, valid.design,
  valid.variable, corType = c("pearson", "bicor")[1], report = T,
  height = 10, width = 8, save.path = "WGCNA", names = "love")

Arguments

object

the result of FastWGCNA

valid.matrix

a list of expression matrix with genes rows and sample cols.

log.convert

whether to do log scale for expression matrix

valid.design

a named list of design object

valid.variable

a named list of trait vector

corType

one of "pearson" and "bicor".Default is pearson

report

whether do a plot report

height

the size of saved plot

width

the size of saved plot

save.path

the space of the save file.Default is "WGCNA"

names

part of saved files name

Value

LuckyWGCNA object

Author(s)

Weibin Huang<654751191@qq.com>

See Also

ModuleTrait.

Examples

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## This is a simulative process and available only with CORRECT VARIABLES
load("E:/RCloud/RFactory/lucky/love/WGCNA-test/love_wgcna.rda")
object = wgcna;rm(wgcna);gc()
log.convert=T
valid.matrix = list(Valid1 = rna.fpkm.tumor,
                    Valid2 = rna.fpkm.tumor)
valid.design = list(Valid1 = rna.design.tumor,
                    Valid2 = rna.design.tumor)
variable = c("age","his1","gender","N.status","T.status")
valid.variable = list(Valid1 = variable,
                      Valid2 = variable)
corType = c("pearson","bicor")[1]
report=F
height = 10;width = 8
save.path = "WGCNA"
names = "love"
result_MTV <- ModuleTraitValid(object,
                               valid.matrix,log.convert=T,
                               valid.design,
                               valid.variable,
                               corType = c("pearson","bicor")[1],
                               height = 10,width = 8,
                               save.path = "WGCNA",
                               names = "love")

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