Description Usage Arguments Value Author(s) References Examples
Survival analysis of modules.
1 2 | moduleSurvival(Modulelist, ExpData, SurvData,
devidePercentage=.5, plot = FALSE)
|
Modulelist |
A list of miRNA sponge modules. |
ExpData |
An input expression data, the columns are genes and the rows are samples. |
SurvData |
An input survival data, three columns contain the information of sample, time (Months) and status, respectively. |
devidePercentage |
A percentage value, the percentage of high risk group. |
plot |
A logical value, plot or not. |
Survival analysis result of modules.
Junpeng Zhang (https://www.researchgate.net/profile/Junpeng_Zhang3)
Terry M. Therneau and Patricia M. Grambsch. Modeling Survival Data: Extending the Cox Model. Springer, New York. ISBN 0-387-98784-3, 2000.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | # Obtain expression data file "ExpData.csv" in csv format
ExpDatacsv <- system.file("extdata","ExpData.csv",package="miRsponge")
ExpData <- read.csv(ExpDatacsv, header=FALSE, sep=",")
# Obtain miRNA-target interaction data file "miR2Target.csv" in csv format
miR2Target <- system.file("extdata", "miR2Target.csv", package="miRsponge")
miRTarget <- read.csv(miR2Target, header=TRUE, sep=",")
# Obtain survival data file "SurvData.csv" in csv format
SurvDatacsv <- system.file("extdata", "SurvData.csv", package="miRsponge")
SurvData <- read.csv(SurvDatacsv, header=TRUE, sep=",")
pcceRInt <- spongeMethod(miRTarget, ExpData, method = "pc")
spongenetwork_Cluster <- netModule(pcceRInt[, 1:2])
sponge_Module_Survival <- moduleSurvival(spongenetwork_Cluster,
ExpData, SurvData)
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