Description Usage Arguments Value Author(s) See Also Examples
View source: R/BI_ModuleTraitValid.R
Get module-trait relationship given new validation cohorts. ModuleTraitValid
supports multiple expression matrix.
1 2 3 | 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")
|
object |
the result of |
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 |
LuckyWGCNA 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 22 23 24 | ## 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")
|
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