dataOvarian: Survival data of 1003 ovarian cancer patients from 4...
In joint.Cox: Joint Frailty-Copula Models for Tumour Progression and Death in Meta-Analysis
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
1
2
3
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.
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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
1 2 3 | 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
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