dataOvarian: Survival data of 1003 ovarian cancer patients from 4...

Description Usage Format Details Source References Examples

Description

The data consist of 1003 surgically treated ovarian cancer patients from four studies (N1=110, N2=58, N3=278, N4=557). Survival outcomes are given to study if the CXCL12 gene expression is a prognostic factor in ovarian cancer. The dataset was used in Emura et al. (2017), which is a subset of the curated ovarian data of Ganzfried et al (2013). We prepared the dataset by using "patientselection.config" in "Curated ovarian data" around May 2015 in the analysis of Emura et al. (2017).

Usage

1
data("dataOvarian")

Format

A data frame with 1003 observations on the following 6 variables.

t.event

: time to event (days from surgery to tumour recurrence)

event

: event indicator (1=recurrence, 0=no recurrence)

t.death

: time to death (days from surgery to death due to any cause)

death

: death indicator (1=death, 0=alive)

group

: study ID; group=4, 8, 11, or 14; see the details below

CXCL12

: CXCL12 gene expression

Details

The data include individual-patient information on 1003 patients from 4 studies (group=4, 8, 11, and 14). The numbers 4, 8, 11 and 14 corresponds to the study IDs from the original data of Ganzfried et al. (2013). "group=4" corresponds to 110 Japanese patients from the study of Yoshihara et al. (2010) (GEO accession number: GSE17260). Other groupds are the studies of GSE30161 (58 patients), GSE9891 (278 patients), and TCGA (557 patients).

Source

Ganzfried BF et al. (2013), Curated ovarian data: clinically annotated data for the ovarian cancer transcriptome, Database, Article ID bat013, doi:10.1093/database/bat013.

References

Emura T, Nakatochi M, Murotani K, Rondeau V (2017), A joint frailty-copula model between tumour progression and death for meta-analysis, Stat Methods Med Res 26(6): 2649-66

Ganzfried BF et al. (2013), Curated ovarian data: clinically annotated data for the ovarian cancer transcriptome, Database, Article ID bat013, doi:10.1093/database/bat013.

Yoshihara K et al. (2010) Gene expression profile for predicting survival in advanced-stage serous ovarian cancer across two independent datasets. PLoS One 12;5(3):e9615

Examples

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data(dataOvarian)
study4=dataOvarian[dataOvarian$group==4,] # extract one study
study4

Example output

Loading required package: survival
          t.event event t.death death group       CXCL12
GSM432220    1650     0    1650     0     4  1.305941603
GSM432221      30     1      30     1     4  1.286216374
GSM432222     720     0     720     0     4 -1.369031455
GSM432223     450     1     780     0     4  1.613269601
GSM432224     510     1     990     1     4  0.611514376
GSM432225    1110     0    1110     0     4 -0.521495322
GSM432226     210     1     600     1     4  0.408670160
GSM432227    1380     1    1410     0     4  0.942074215
GSM432228    1800     0    1800     0     4 -0.927825123
GSM432229     540     1    1710     1     4  0.373056663
GSM432230    1440     0    1440     0     4 -1.453803350
GSM432231    1290     1    2070     0     4 -1.267301039
GSM432232     240     1     810     1     4 -0.424467894
GSM432233     360     1    2070     1     4 -0.749748399
GSM432234     420     1    1530     1     4 -0.358063075
GSM432235     510     0     510     0     4  0.129403055
GSM432236     240     1     510     0     4 -0.526008894
GSM432237     510     0     510     0     4  1.568904151
GSM432238     240     1     720     1     4  0.028281225
GSM432239     180     1    1560     1     4 -1.196361903
GSM432240     240     1     750     1     4  0.746859775
GSM432242     450     1     660     1     4 -1.379081807
GSM432243     690     1    1590     1     4 -1.189039075
GSM432244     360     1     390     1     4 -0.502489768
GSM432245     750     1    2370     0     4 -0.087862283
GSM432246    2220     0    2220     0     4  0.960581126
GSM432247    2250     0    2250     0     4 -0.929019593
GSM432248     900     1    1860     1     4 -0.554676687
GSM432249    1920     0    1920     0     4  0.331672641
GSM432250    1380     0    1380     0     4  1.073596997
GSM432251    1050     1    1320     0     4  0.662998826
GSM432252     420     1     840     1     4  0.705235072
GSM432253     180     1     990     0     4  2.079427691
GSM432254     780     1     930     0     4 -0.421188802
GSM432255     720     1     840     0     4  1.531747540
GSM432256     720     0     720     0     4 -0.685830376
GSM432257     450     0     450     0     4  0.057503513
GSM432258     450     0     450     0     4  1.078396187
GSM432259     540     1    1470     0     4  0.781676412
GSM432260     420     0     420     0     4 -1.045002196
GSM432261     390     0     390     0     4 -2.239107887
GSM432262     270     1     270     0     4 -0.602097863
GSM432263     870     0     870     0     4 -1.264563733
GSM432264     780     0     780     0     4 -1.440523933
GSM432265     390     1    1470     0     4 -1.505642143
GSM432266     480     1     600     0     4 -0.099683169
GSM432267    1410     0    1410     0     4 -0.113879171
GSM432268      90     1     450     1     4  2.107384943
GSM432269      60     1     360     1     4 -0.750336276
GSM432270     150     1     780     1     4  1.191027405
GSM432271     690     1    1230     1     4  1.920500394
GSM432272      30     1     330     1     4  0.001307381
GSM432273     510     1    1410     1     4  1.488599321
GSM432274    1500     0    1500     0     4 -1.390286057
GSM432275      30     1      30     1     4  1.380971665
GSM432276    2160     0    2160     0     4 -0.154641934
GSM432277    1950     0    1950     0     4  0.121887322
GSM432278     600     1     990     0     4 -0.657578268
GSM432279     360     1     870     0     4  1.545653353
GSM432280     540     1    1470     1     4  0.434848266
GSM432281    2100     0    2100     0     4 -0.253577506
GSM432282     450     0     450     0     4 -0.917347010
GSM432283      60     1     240     1     4 -0.695820836
GSM432284     870     1    2400     1     4 -0.963525900
GSM432285     240     1     330     1     4  1.157072690
GSM432286      60     1     150     1     4 -0.381232698
GSM432287     690     1     840     1     4 -0.370147672
GSM432288     630     1     750     1     4  0.857411841
GSM432289     450     1    1920     1     4 -1.129397167
GSM432290      60     1    1230     1     4 -1.877195397
GSM432291    1830     0    1830     0     4  0.245603578
GSM432292     510     1    1380     0     4 -0.682438979
GSM432293     210     1    1020     1     4 -1.090402060
GSM432294     120     1     510     1     4  0.096917209
GSM432295    1050     1    1170     0     4 -1.334536982
GSM432296     990     1    1110     0     4 -0.562312773
GSM432297     240     1     990     1     4  0.146260918
GSM432298     420     1     750     0     4  0.825708468
GSM432299     120     1     720     0     4  1.791953220
GSM432300     270     1     690     1     4  1.114043048
GSM432301     900     0     900     0     4 -0.730840171
GSM432302     900     0     900     0     4 -0.743920832
GSM432303     420     1     870     0     4  0.994777646
GSM432304     360     1     690     0     4  0.696917800
GSM432305     390     1     600     0     4  0.315535071
GSM432306     360     1     960     1     4 -1.023094391
GSM432307    1410     1    2430     0     4  1.720215014
GSM432308     780     1    2220     0     4 -1.271656892
GSM432309     330     1     780     1     4 -0.454306834
GSM432310     780     0     780     0     4  1.272696300
GSM432311     570     0     570     0     4  1.158343413
GSM432312     660     0     660     0     4 -1.329647409
GSM432313     660     0     660     0     4 -0.152836271
GSM432314     630     0     630     0     4 -0.529723866
GSM432315     570     1    1260     1     4 -0.300945111
GSM432316     390     1     780     1     4  0.560129486
GSM432317      30     1      30     1     4  0.633933200
GSM432318     480     1     810     1     4 -1.505859495
GSM432319     360     1    2040     1     4  0.500369846
GSM432320     840     1    1920     0     4  0.830043552
GSM432321    1560     0    1560     0     4 -0.288380885
GSM432322    1530     1    1950     0     4  0.923434296
GSM432323     390     1     990     1     4 -1.310321201
GSM432324     870     1    1530     1     4  0.354078756
GSM432325      30     1      30     1     4  0.897661008
GSM432326      90     1    1620     1     4 -0.126274690
GSM432327    1530     0    1530     0     4  0.666736856
GSM432328     600     1    1530     0     4 -0.268661946
GSM432329     120     1    1170     0     4 -0.511818633
GSM432330     240     1     840     0     4  0.383810614

joint.Cox documentation built on Feb. 4, 2022, 5:08 p.m.