Description Usage Arguments Value See Also Examples
Calculate hazard ratio of miRNAs or mRNAs from a corObject using a Cox proportional hazards regression.
1 |
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 |
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)
package:survival
, coxph
, plotSurv
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | 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)
minimal@pheno.miRNA$time<-runif(nrow(minimal@pheno.miRNA),1,20)
minimal@pheno.miRNA$event<-rbinom(nrow(minimal@pheno.miRNA),1,0.5)
minimal@pheno.miRNA$a1<-rnorm(nrow(minimal@pheno.miRNA),1,0.5)
minimal@pheno.miRNA$a2<-rnorm(nrow(minimal@pheno.miRNA),1,0.5)
#plotSurv(minimal, "miRNA", "hsa-let-7c", "time", "event")
minimal.diffexp<-addSurv(minimal, "miRNA", "time", "event",c("a1","a2"))
head(minimal.diffexp@diffexp.miRNA)
minimal.diffexp<-addSurv(minimal, "miRNA", "time", "event",c("a1"))
head(minimal.diffexp@diffexp.miRNA)
minimal.diffexp<-addSurv(minimal, "miRNA", "time", "event")
head(minimal.diffexp@diffexp.miRNA)
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