ModuleSurvValid: Get module-Survival relationship given new validation cohorts

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

Description

Get module-Survival relationship given new validation cohorts

Usage

ModuleSurvValid(object, valid.matrix, log.convert = T, valid.design,
  valid.time, valid.status, digits = 3, 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.time	a named list of time colnames
valid.status	a named list of status colnames
digits	integer indicating the number of decimal places (round) or significant digits (signif) to be used. Negative values are allowed (see ‘Details’).
save.path	the space of the save file.Default is "WGCNA"
names	part of saved files name

Value

LuckyWGCNA object

Author(s)

Weibin Huang<[e-mail]>

See Also

ModuleSurv.

Examples

## 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)
time = c("OS.time","DFS.time")
status = c("OS.status","DFS.status")
valid.time = list(Valid1 = time,
                  Valid2 = time)
valid.status = list(Valid1 = status,
                    Valid2 = status)
save.path = "WGCNA"
names = "love"
digits = 3
result_MSV <- ModuleSurvValid(object,
                              valid.matrix,
                              log.convert=T,
                              valid.design,
                              valid.time,
                              valid.status,
                              digits = 3,
                              save.path = "WGCNA",
                              names = "love")

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