BI_extra.surv: Get survival data of a gene based on expression and design...

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

Description

extra.surv help get survival data of a gene based on expression and design objects.Note that multiple genes would not be supported.

Usage

extra.surv(expr.matrix,
                 design,
                 select,
                 event.status,
                 event.time,
                 event.lower,
                 mode=c("median","maxstat")[1])

Arguments

expr.matrix	expression matrix
design	design object
select	a gene.Multiple genes are not supported
event.status	a colname of status
event.time	a colname of time
event.lower	the lower limit of the time
mode	Default is "median".You can also set a number of percentum or a decimal less than 1.When mode = "maxstat",the maxstat automatical selected cut-off strategy would be used

Value

a list containing P value of significant in univariate cox model and the metadata of survival information and binary gene expression

Author(s)

Weibin Huang<[e-mail]>

Examples

## This is a simulative process and NOT RUN
expr.matrix=train.fpkm
design = design.train
select = rocgenes[1]
event.status = "DFS.status"
event.time = "DFS.time"
event.lower = 89
mode="median"

## method = "median"
l1 <- extra.surv(expr.matrix,
                 design,
                 select,
                 event.status,
                 event.time,
                 event.lower,
                 mode="median")

## method = "maxstat"
l1 <- extra.surv(expr.matrix,
                 design,
                 select,
                 event.status,
                 event.time,
                 event.lower,
                 mode="maxstat")

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