Description Usage Arguments Details Value Author(s) Examples
cox.optimized3 help select prognosis-predictive genes base on expression matrix and related design object
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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 |
cox.optimized3 depends on survival package and some parrallel algrithm
a list containing cox model genes and related cox result
Weibin Huang<654751191@qq.com>
1 2 3 4 5 6 7 8 9 10 11 12 13 | ## 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)}
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