BI_cox.optimized4: get survival significant markers based on KM-Curve data

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

Description

cox.optimized4 help get survival significant markers based on KM-Curve data

Usage

cox.optimized4(expr.matrix,
               design,
               time.col,
               status.col,
               strategy  = c("median","maxstat")[1],
               smethod="LogRank",
               pmethod="HL",
               cutoff.p = 0.05,
               digits = 5,
               parallel = F)

Arguments

expr.matrix	expression matrix
design	design object
time.col	colname of time value
status.col	colname of status value
strategy	one of "median" and "maxstat"
smethod	Default is "LogRank"
pmethod	Default is "HL"
cutoff.p	p value cut-off
digits	digits of result
parallel	whether to use parallel strategy when strategy is median.Note that the parallel would always be applied with maxstat method

Note

the maxstat function depends on maxstat package.Parameters like smethod and pmethod are belongs to maxstat function.

Author(s)

Weibin Huang<[e-mail]>

See Also

maxstat::maxstat.test

Examples

## This is a simulative process and NOT RUN
cox.optimized4(expr.matrix,
               design,
               time.col,
               status.col,
               strategy  = "median",
               cutoff.p = 0.05,
               digits = 5,
               parallel = T)

## This is a simulative process and NOT RUN
cox.optimized4(expr.matrix,
               design,
               time.col,
               status.col,
               strategy  = "maxstat",
               smethod="LogRank",
               pmethod="HL",
               cutoff.p = 0.05,
               digits = 5)

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