moduleSurvival: Survival analysis of modules

Description Usage Arguments Value Author(s) References Examples

View source: R/miRsponge.R

Description

Survival analysis of modules.

Usage

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moduleSurvival(Modulelist, ExpData, SurvData,
devidePercentage=.5, plot = FALSE)

Arguments

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.

Value

Survival analysis result of modules.

Author(s)

Junpeng Zhang (https://www.researchgate.net/profile/Junpeng_Zhang3)

References

Terry M. Therneau and Patricia M. Grambsch. Modeling Survival Data: Extending the Cox Model. Springer, New York. ISBN 0-387-98784-3, 2000.

Examples

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# 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)

zhangjunpeng411/miRsponge documentation built on April 19, 2018, 9:07 a.m.