addSurv: Calculate hazard ratio

In mariavica/mircomb: An R package for analyzing miRNA-mRNA interactions

Description

Calculate hazard ratio of miRNAs or mRNAs from a corObject using a Cox proportional hazards regression.

Usage

addSurv(obj, dataset, time, event, adjusting = NULL)

Arguments

obj	a corObject
dataset	"miRNA" or "mRNA".
time	colname of the time column in the pheno.miRNA or pheno.mRNA slot
event	colname of the event column in the pheno.miRNA or pheno.mRNA slot
adjusting	(optional) colname of the adjusting variables that will be used

Value

a corObject with a diffexp.miRNA or diffexp.mRNA slot added. The slot is a data.frame in which row names are the names of the miRNAs or mRNAs and has the following columns:

• coef: risk associated to the expression of the miRNA/mRNA

• pval: p values

• adj.pval: p values corrected for multiple testing (FDR)

See Also

package:survival, coxph, plotSurv

Examples

data(miRNA)
data(mRNA)
data(pheno.miRNA)
data(pheno.mRNA)

minimal<-new("corObject",dat.miRNA=miRNA,dat.mRNA=mRNA,
	pheno.miRNA=pheno.miRNA,pheno.mRNA=pheno.mRNA)

[e-mail]$time<-runif(nrow([e-mail]),1,20)
[e-mail]$event<-rbinom(nrow([e-mail]),1,0.5)
[e-mail]$a1<-rnorm(nrow([e-mail]),1,0.5)
[e-mail]$a2<-rnorm(nrow([e-mail]),1,0.5)


#plotSurv(minimal, "miRNA", "hsa-let-7c", "time", "event")

minimal.diffexp<-addSurv(minimal, "miRNA", "time", "event",c("a1","a2"))
head([e-mail])
minimal.diffexp<-addSurv(minimal, "miRNA", "time", "event",c("a1"))
head([e-mail])
minimal.diffexp<-addSurv(minimal, "miRNA", "time", "event")
head([e-mail])

mariavica/mircomb documentation built on Feb. 3, 2020, 2:28 a.m.