Nothing
## ----echo=FALSE,include=FALSE-------------------------------------------------
library(simPATHy)
library(graph)
## ----eval=FALSE---------------------------------------------------------------
# library(simPATHy)
# library(graph)
## -----------------------------------------------------------------------------
data("chimera")
dim(chimera)
table(colnames(chimera))
## -----------------------------------------------------------------------------
graph<-gRbase::dag(~867:25+867:613+5295:867+5294:867+
207:5295+207:5294+4193:207+3551:207+
4792:3551+7157:4193+3265:6654+
3845:6654+6654:2885+2885:25+2885:613)
## -----------------------------------------------------------------------------
genes<-graph::nodes(graph)
data<-t(chimera[genes,colnames(chimera)==1])
S<-cov(data)
## -----------------------------------------------------------------------------
S<-fitSgraph(graph,S)
round(S[1:5,1:5],3)
## ---- eval=FALSE--------------------------------------------------------------
# plotGraphNELD3(graph,type = "cor",S1 = S)
## ---- fig.height=5, fig.width=7, fig.align='center'--------------------------
plotCorGraph(S1 = S,type = "cor")
## ---- fig.height=5, fig.width=7, fig.align='center'--------------------------
lim<-round(max(abs(simPATHy:::riscala(S))[upper.tri(S)]),2)
plotCorGraph(S1 = S,type ="cor",colLim = c(-lim,lim))
## ---- fig.height=5, fig.width=7, fig.align='center'--------------------------
plotCorGraph(S1 = S,type = "cor", graph = graph)
## -----------------------------------------------------------------------------
path<-list(c("613","867"),c("867","5295"),c("5295","207"),
c("207","4193"),c("4193","7157"))
## ---- eval=FALSE--------------------------------------------------------------
# path <- getPathShiny(graph)
## -----------------------------------------------------------------------------
path
## ---- eval=FALSE--------------------------------------------------------------
# path <- generatePath(graph,from="613",to="7157")
## ---- eval=FALSE--------------------------------------------------------------
# path1 <- list(c("613","2885"), c("4193","7157"))
## -----------------------------------------------------------------------------
min<-c(2,8,2,0.1,0.5)
max<-c(2,10,2,4,0.5)
## -----------------------------------------------------------------------------
prob<-c(1,0,0,0.5,1)
dys<-cbind(min,max,prob)
rownames(dys)<-sapply(path,paste,collapse = "~")
dys
## -----------------------------------------------------------------------------
set.seed(123)
Result<-simPATHy(graph,path,S,min,max,prob)
## -----------------------------------------------------------------------------
class(Result)
names(Result)
## -----------------------------------------------------------------------------
round(Result$dataset[c(1:3,501:503),1:5],3)
## -----------------------------------------------------------------------------
Result$param
## -----------------------------------------------------------------------------
Result$strength
## -----------------------------------------------------------------------------
Result$correction
## ----eval = FALSE-------------------------------------------------------------
# easyLookDys(Result)
## ----echo= FALSE--------------------------------------------------------------
knitr::kable(easyLookDys(Result))
## ---- fig.height=5, fig.width=7, fig.align='center'--------------------------
plotCorGraph(S1 = Result$S1, S2 = Result$S2, type = "cor",
graph = graph, path = Result$path,colLim = c(-0.4,0.4))
## ---- eval=FALSE--------------------------------------------------------------
# easyLookShiny(Result, graph)
## ----echo=TRUE, message=FALSE, warning=FALSE, eval=FALSE----------------------
# library(topologyGSA)
# #?pathway.var.test
# y1<-Result$dataset[rownames(Result$dataset)=="cl1",]
# y2<-Result$dataset[rownames(Result$dataset)=="cl2",]
# alpha<-0.05
# pathway.var.test(y1, y2, dag = graph, alpha)
## ----echo=TRUE, message=FALSE, warning=FALSE, eval=FALSE----------------------
# library(clipper)
# #?clipper
# expr<-t(Result$dataset)
# classes<-as.numeric(gsub("cl","",colnames(expr)))
# clipped<-clipper(expr,classes,graph)
# clipped
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