Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
require(psSubpathway)
## -----------------------------------------------------------------------------
# load depend package.
require(GSVA)
require(parallel)
# get breast cancer disease subtype gene expression profile.
Bregenematrix<-get("Subgenematrix")
# get path of the sample disease subtype files.
Subtypelabels<- system.file("extdata", "Sublabels.cls", package = "psSubpathway")
# perform the SubSEA method.
#SubSEAresult<-SubSEA(Bregenematrix,
# input.cls=Subtypelabels,
# nperm=50, # Number of random permutations
# fdr.th=0.01, # Cutoff value for fdr.when fdr.th=1,get all subpathway
# parallel.sz=2) # Number of processors to use
# get the result of the SubSEA function
SubSEAresult<-get("Subspwresult")
str(SubSEAresult)
head(SubSEAresult$Basal)
## ----message=FALSE, warning=FALSE---------------------------------------------
# load depend package.
require(mpmi)
# get ACC disease stage gene expression profiling.
ACCgenematrix<-get("DCgenematrix")
# get path of the sample disease stage phenotype files.
Stagelabels<-system.file("extdata", "DClabels.cls", package = "psSubpathway")
# perform the DCSA method.
#DCSAresult<-DCSA(ACCgenematrix,input.cls=Stagelabels,nperm=50,fdr.th=0.01,parallel.sz=2)
# get the result of the SubSEA function
DCSAresult<-get("DCspwresult")
str(DCSAresult)
head(DCSAresult$DCSA)
## ----fig.height=3, fig.width=12-----------------------------------------------
# plot enrichment score curve of the subpathway 00120_9 in all breast cancer subtypes
plotSubSEScurve(Subspwresult,
spwid="00120_9", # The subpathway id which subpahtway is ploted
phenotype="all") # Which phenotypic phenotype set enrichment curve is drawn
## ----fig.height=4, fig.width=5------------------------------------------------
# plot enrichment score curve of the subpathway 00120_9 in the Basal breast cancer subtype.
plotSubSEScurve(Subspwresult,spwid="00120_9",phenotype="Basal")
## ----fig.height=6, fig.width=10-----------------------------------------------
# plot the subpathway 00120_9 in the SubSEA function result.
plotSpwACmap(Subspwresult,spwid="00120_9")
## ----fig.height=6, fig.width=10-----------------------------------------------
# plot the subpathway 00982_2 in the DCSA function result.
plotSpwACmap(DCspwresult,spwid="00982_2")
## ----fig.height=8, fig.width=10-----------------------------------------------
# load depend package.
require(pheatmap)
# plot significant up-regulation subpathway heat map specific for each breast cancer subtype.
plotheatmap(Subspwresult,
fdr.th=0.01, # Cutoff value for fdr
plotSubSEA=TRUE, # Indicate that the input data is the result of the SubSEA function
SES="positive", # Obtain a subpathway with a positive SES value
phenotype="all")
## ----fig.height=8, fig.width=10-----------------------------------------------
# plot significant down-regulation subpathway heat map specific for each breast cancer subtype.
plotheatmap(Subspwresult,plotSubSEA=TRUE,fdr.th=0.01,SES="negative",phenotype="all")
## ----fig.height=8, fig.width=10-----------------------------------------------
# plot Basal subtype specific significant subpathway heat map.
plotheatmap(Subspwresult,plotSubSEA=TRUE,fdr.th=0.01,SES="all",phenotype="Basal")
## ----fig.height=8, fig.width=10-----------------------------------------------
# plot a heat map of the subpathway that is significantly associated with breast cancer stages.
plotheatmap(DCspwresult,plotSubSEA=FALSE,fdr.th=0.01)
## ----fig.height=6, fig.width=7------------------------------------------------
# get the Subspwresult which is the result of SubSEA method.
Subspwresult<-get("Subspwresult")
# plot significant heat map between the activity of the subpathway in each subtype of breast cancer.
plotSpwPSheatmap(Subspwresult,spwid="00120_9")
## ----fig.height=6, fig.width=7------------------------------------------------
# get the DCspwresult which is the result of DCSA method.
DCspwresult<-get("DCspwresult")
##' # plot significant heat map between the activity of the subpathway in each stage of breast cancer.
plotSpwPSheatmap(DCspwresult,spwid="00982_2")
## ----fig.height=6, fig.width=8, message=FALSE, warning=FALSE------------------
# load depend package.
library(igraph)
# plot network graph of the subpathway 00982_2
plotSpwNetmap("00982_2")
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