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\T1/ptm/m/n/10 Kains \T1/pcr/m/n/10 <bhaibeka@jimmy.harvard.edu>\T1/ptm/m/n/10
, Markus Schroeder \T1/pcr/m/n/10 <mschroed@jimmy.harvard.edu>
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[]\T1/ptm/m/n/10 - Com-pu-ta-tional Bi-ol-ogy and Func-tional Ge-nomics Lab-o-r
a-tory, Dana-Farber Can-cer In-sti-tute, Boston,
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[]\T1/ptm/m/n/10 - Com-pu-ta-tional Bi-ol-ogy and Func-tional Ge-nomics Lab-o-r
a-tory, Dana-Farber Can-cer In-sti-tute, Boston,
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[][][]$\T1/pcr/m/n/10 http : / / www . cebitec . uni-[]bielefeld . de / cebitec
/ computational-[]genomics /
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[]\T1/pcr/m/n/10 survival\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Hmisc\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 Design\T1/ptm/m/n/10 , \T1/pcr/m/n/10 prodlim\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 survivalROC\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ipred\T1/ptm/m/n/10 , \
T1/pcr/m/n/10 bootstrap\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CPE\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 clinfun
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[]\T1/pcr/m/n/10 exprs(mainz7g)\T1/ptm/m/n/10 : Ma-trix con-tain-ing gene ex-pr
es-sions as mea-sured by Affymetrix hgu133a
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[]\T1/pcr/m/n/10 experimentalData(mainz7g)\T1/ptm/m/n/10 : MI-AME ob-ject con-t
ain-ing in-for-ma-tion about the dataset.
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[]\T1/ptm/m/n/10 The func-tion com-bines sev-eral es-ti-ma-tors us-ing meta-ana
lytical for-mula to com-pute a meta-estimate.
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[18]
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\T1/ptm/m/n/10 and ran-dom ef-fects meta-analysis for two-sample com-par-isons
and cu-mu-la-tive meta-analyses. Draws
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[20]
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[]\T1/ptm/m/n/10 list of data used to com-pute the haz-ard ra-tio (\T1/pcr/m/n/
10 x\T1/ptm/m/n/10 , \T1/pcr/m/n/10 surv.time \T1/ptm/m/n/10 and \T1/pcr/m/n/10
surv.event\T1/ptm/m/n/10 ).
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=c(0.45,0.6,0.63), labels=c("A","B","C"), xlim=c(0.2,0.8), boxsize=0.5, zero=0.
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\T1/ptm/m/n/10 dard er-ror for sen-si-tiv-ity and speci-ficity is es-ti-mated t
hrough jack-knife pro-ce-dure (see [][]\T1/pcr/m/n/10 jackknife[][][]\T1/ptm/m/
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[]\T1/ptm/m/n/10 This dataset con-tains a sub-set of the gene ex-pres-sion, an-
no-ta-tions and clin-i-cal data from the TRANS-
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\T1/ptm/m/n/10 Kains \T1/pcr/m/n/10 <bhaibeka@jimmy.harvard.edu>\T1/ptm/m/n/10
, Markus Schroeder \T1/pcr/m/n/10 <mschroed@jimmy.harvard.edu>
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[]\T1/ptm/m/n/10 - Com-pu-ta-tional Bi-ol-ogy and Func-tional Ge-nomics Lab-o-r
a-tory, Dana-Farber Can-cer In-sti-tute, Boston,
[2]
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[]\T1/ptm/m/n/10 - Com-pu-ta-tional Bi-ol-ogy and Func-tional Ge-nomics Lab-o-r
a-tory, Dana-Farber Can-cer In-sti-tute, Boston,
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[][][]$\T1/pcr/m/n/10 http : / / www . cebitec . uni-[]bielefeld . de / cebitec
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[]\T1/pcr/m/n/10 survival\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Hmisc\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 Design\T1/ptm/m/n/10 , \T1/pcr/m/n/10 prodlim\T1/ptm/m/n/10 , \T
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T1/pcr/m/n/10 bootstrap\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CPE\T1/ptm/m/n/10 , \T1/
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[]\T1/pcr/m/n/10 exprs(mainz7g)\T1/ptm/m/n/10 : Ma-trix con-tain-ing gene ex-pr
es-sions as mea-sured by Affymetrix hgu133a
[3]
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[]\T1/pcr/m/n/10 experimentalData(mainz7g)\T1/ptm/m/n/10 : MI-AME ob-ject con-t
ain-ing in-for-ma-tion about the dataset.
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[]\T1/ptm/m/n/10 The func-tion com-bines sev-eral es-ti-ma-tors us-ing meta-ana
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\T1/ptm/m/n/10 and ran-dom ef-fects meta-analysis for two-sample com-par-isons
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[]\T1/ptm/m/n/10 This dataset con-tains a sub-set of the gene ex-pres-sion, an-
no-ta-tions and clin-i-cal data from the TRANS-
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\T1/ptm/m/n/10 Kains \T1/pcr/m/n/10 <bhaibeka@jimmy.harvard.edu>\T1/ptm/m/n/10
, Markus Schroeder \T1/pcr/m/n/10 <mschroed@jimmy.harvard.edu>
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[]\T1/ptm/m/n/10 - Com-pu-ta-tional Bi-ol-ogy and Func-tional Ge-nomics Lab-o-r
a-tory, Dana-Farber Can-cer In-sti-tute, Boston,
[2]
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[]\T1/ptm/m/n/10 - Com-pu-ta-tional Bi-ol-ogy and Func-tional Ge-nomics Lab-o-r
a-tory, Dana-Farber Can-cer In-sti-tute, Boston,
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[][][]$\T1/pcr/m/n/10 http : / / www . cebitec . uni-[]bielefeld . de / cebitec
/ computational-[]genomics /
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[]\T1/pcr/m/n/10 survival\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Hmisc\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 Design\T1/ptm/m/n/10 , \T1/pcr/m/n/10 prodlim\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 survivalROC\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ipred\T1/ptm/m/n/10 , \
T1/pcr/m/n/10 bootstrap\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CPE\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 clinfun
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[]\T1/pcr/m/n/10 exprs(mainz7g)\T1/ptm/m/n/10 : Ma-trix con-tain-ing gene ex-pr
es-sions as mea-sured by Affymetrix hgu133a
[3]
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[]\T1/pcr/m/n/10 experimentalData(mainz7g)\T1/ptm/m/n/10 : MI-AME ob-ject con-t
ain-ing in-for-ma-tion about the dataset.
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[]\T1/pcr/m/n/9 cindex.comp.meta(list.cindex1=list("cindex.age1"=c1.1, "cindex
.age2"=c1.2),[]
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[]\T1/ptm/m/n/10 The func-tion com-bines sev-eral es-ti-ma-tors us-ing meta-ana
lytical for-mula to com-pute a meta-estimate.
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[]\T1/pcr/m/n/10 combine.test(p, weight, method = c("fisher", "z.transform", "
logit"),[]
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[]\T1/pcr/m/n/10 concordance.index(x, surv.time, surv.event, cl, weights, comp
pairs=10, strat,[]
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[] \T1/pcr/m/n/10 alpha = 0.05, outx = TRUE, method = c("conservative", "noet
her", "nam"),[]
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[]\T1/pcr/m/n/9 D.index(x=age, surv.time=stime, surv.event=sevent, weights=wei
ght, strat=strat)[]
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[]\T1/pcr/m/n/9 dindex.comp.meta(list.dindex1=list("dindex.age1"=d1.1, "dindex
.age2"=d1.2),[]
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[] \T1/pcr/m/n/10 graphwidth = unit(2, "inches"), col = meta.colors(), xlog =
FALSE,[]
[19]
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\T1/ptm/m/n/10 and ran-dom ef-fects meta-analysis for two-sample com-par-isons
and cu-mu-la-tive meta-analyses. Draws
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[]\T1/pcr/m/n/10 hazard.ratio(x, surv.time, surv.event, weights, strat, alpha
= 0.05,[]
[21]
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[]\T1/ptm/m/n/10 list of data used to com-pute the haz-ard ra-tio (\T1/pcr/m/n/
10 x\T1/ptm/m/n/10 , \T1/pcr/m/n/10 surv.time \T1/ptm/m/n/10 and \T1/pcr/m/n/10
surv.event\T1/ptm/m/n/10 ).
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[] \T1/pcr/m/n/9 stop("the two vector of BSCs must be computed for the same p
oints in time!") }[]
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[] \T1/pcr/m/n/10 o.text, v.line, h.line, .col = 1:4, .lty = 1, .lwd = 1, sho
w.n.risk = FALSE,[]
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[] \T1/pcr/m/n/9 .lty=c(1,1,1), show.n.risk=TRUE, n.risk.step=2, n.risk.cex=0
.85, verbose=FALSE)[]
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[]\T1/pcr/m/n/10 logpl(pred, surv.time, surv.event, strata, na.rm = FALSE, ver
bose = FALSE)[]
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[]\T1/pcr/m/n/9 logpl(pred=predict(object=coxm, newdata=dd), surv.time=stime,
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[]\T1/pcr/m/n/10 exprs(mainz7g)\T1/ptm/m/n/10 : Ma-trix con-tain-ing gene ex-pr
es-sions as mea-sured by Affymetrix hgu133a
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[]\T1/pcr/m/n/10 experimentalData(mainz7g)\T1/ptm/m/n/10 : MI-AME ob-ject con-t
ain-ing in-for-ma-tion about the dataset.
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[] \T1/pcr/m/n/10 labels=NULL, conf.level = .95, xlab = "", ylab = "", xlim
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[]\T1/pcr/m/n/9 metaplot.surv(mn=c(0.4,0.5,0.6), lower=c(0.35,0.4,0.57), upper
=c(0.45,0.6,0.63), labels=c("A","B","C"), xlim=c(0.2,0.8), boxsize=0.5, zero=0.
5, col=meta.colors(box="royalblue",line="darkblue",zero="firebrick"))[]
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[]\T1/pcr/m/n/10 sbrier.score2proba(data.tr, data.ts, method = c("cox", "prodl
im"))[]
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[]\T1/pcr/m/n/10 td.sens.spec(cl, surv.time, surv.event, time, span = 0, sampl
ing = FALSE,[]
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\T1/ptm/m/n/10 dard er-ror for sen-si-tiv-ity and speci-ficity is es-ti-mated t
hrough jack-knife pro-ce-dure (see [][]\T1/pcr/m/n/10 jackknife[][][]\T1/ptm/m/
n/10 ).
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[]\T1/pcr/m/n/10 tdrocc(x, surv.time, surv.event, surv.entry = NULL, time, cut
pts = NA,[]
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[]\T1/ptm/m/n/10 This dataset con-tains a sub-set of the gene ex-pres-sion, an-
no-ta-tions and clin-i-cal data from the TRANS-
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