GetWGCNATrait: create trait matrix for WGCNA

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

Description

GetWGCNATrait creates trait matrix for WGCNA.If there are some factor variables in your design object,they must be converted into numeric vector before go into ModuleTrait function,when GetWGCNATrait would complete this job.

Usage

GetWGCNATrait(design, convert.list)

Arguments

design	design object
convert.list	a list of convert information.See examples.

Value

a new design object

Author(s)

Weibin Huang<[e-mail]>

Examples

library(lucky)
data(rna.design.tumor)
stad.convert.list <- {list(
condition = list("tumor" = 1,"normal" = 0),
Mol.subtype = list("EMT" = 3,"MSI" = 2,"MSS/TP53-" = 0,"MSS/TP53+" = 1),
Mol.subtype2 = list("MSI-H" = 2,"MSI-L"=1,"MSS" = 0),
TCGA.subtype = list("CIN"=1,"EBV"=2,"GS"=3,"MSI"=4),
gender = list("FEMALE"=0,"MALE"=1),
his1 = list("Intestinal Adenocarcinoma"=0,"Adenocarcinoma" =1,"Signet Ring Type"=2),
his2 = list("Not Otherwise Specified (NOS)"=0,"Papillary Type"=1,"Tubular Type"=2,"Mucinous Type"=3,"Diffuse Type"=4),
his.grade = list("GX"=0,"G1"=1, "G2"=2, "G3"=3),
pStage = list("Stage I"=1,"Stage IA"=1,"Stage IB"=1,
             "Stage II"=2,  "Stage IIA"=2,  "Stage IIB" =2,
             "Stage III" =3,"Stage IIIA"=3, "Stage IIIB"=3,
             "Stage IIIC"=3, "Stage IV"=4),
pT = list("T1"=1, "T2"=2, "T3"=3, "T4"=4),
T.status = list("T_early"=0,"T_later"=1),
N.status = list("N0"=0, "Np"=1),
M.status  = list("M0"=0, "M1" =1,"MX"=NA)
)}
stad.Trait <- GetWGCNATrait(design,stad.convert.list)

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