Description Usage Arguments Value Author(s) Examples
View source: R/BI_GetWGCNATrait.R
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.
1 | GetWGCNATrait(design, convert.list)
|
design |
design object |
convert.list |
a list of convert information.See examples. |
a new design object
Weibin Huang<654751191@qq.com>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | 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)
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