BI_cox.optimized3: select prognosis-predictive genes

In shijianasdf/BasicBioinformaticsAnalysisFromZhongShan: Launch Usual Clinical tool for Kind Yield

Description

cox.optimized3 help select prognosis-predictive genes base on expression matrix and related design object

Usage

cox.optimized3(expr.matrix,
               design,
               sd.cutoff = NULL,
               p.cutoff = 0.0001,
               FDR.cutoff = NULL,
               event.status=c("TTR.status","DFS.status","OS.status"),
               event.time=c("TTR.time","DFS.time","OS.time"),
               event.lower =c(89,89,89),
               show.music =T)

Arguments

expr.matrix	expression matrix
design	design object

sd.cutoff

sd.cutoff	the cut-off of standard deviation.Default is NULL,and you can set a number if you want to use a sd filter
p.cutoff	the cut-off of P value.Default is 0.0001
FDR.cutoff	the cut-off of BH adjusted P value.Default is 0.001.If NULL,the FDR filter would not be applied
event.status	character, the colnames of event status
event.time	]character.the colnames of event time
event.lower	numeric.the lower border of time
show.music	whether show music at the end of the programe

Details

cox.optimized3 depends on survival package and some parrallel algrithm

Value

a list containing cox model genes and related cox result

Author(s)

Weibin Huang<[e-mail]>

Examples

## This is a simulative process and NOT RUN
cox.model <- cox.optimized3(expr.matrix,
                            design,
                            p.cutoff = 0.0001,
                            FDR.cutoff = 0.001,
                            event.status=c("TTR.status","DFS.status","OS.status"),
                            event.time=c("TTR.time","DFS.time","OS.time"),
                            event.lower =c(89,89,89))
save(cox.model,file = "seed35_cox.model.rda")

## Garbage management
garbage = c("expr.matrix1","design1","event.status.i","event.time.i","event.lower.i")
for(n in garbage){rm(list = ls(pattern = n),envir = .GlobalEnv)}

shijianasdf/BasicBioinformaticsAnalysisFromZhongShan documentation built on Jan. 3, 2020, 10:08 p.m.