![[Experimental]](figures/lifecycle-experimental.svg)
This is a useful function when trying to join genetic with CDISC data sets.
Usage
inner_join_cdisc(
gene_data,
cdisc_data,
patient_key = "USUBJID",
additional_keys = character()
)Arguments
- gene_data
(
data.frameorDataFrame)
genetic data.- cdisc_data
(
data.frame)
CDISC data (typically patient level data).- patient_key
(
string)
patient identifier.- additional_keys
(
character)
potential additional keys for the two data sets.
Note
Columns which are contained in both data sets but are not specified as keys are taken
from gene_data and not from cdisc_data.
Examples
gene_data <- col_data_with_genes(hermes_data, "counts", gene_spec("GeneID:1820"))
cdisc_data <- data.frame(
USUBJID = head(gene_data$USUBJID, 10),
extra = 1:10
)
result <- inner_join_cdisc(gene_data, cdisc_data)
#> Warning: Patients AB12345-CHN-7-id-28, AB12345-CHN-4-id-73, AB12345-RUS-1-id-52, AB12345-PAK-11-id-268, AB12345-CHN-13-id-102, AB12345-CHN-17-id-84, AB12345-BRA-11-id-9, AB12345-CHN-4-id-115, AB12345-CHN-15-id-245, AB12345-CHN-4-id-370 from gene data set were lost because they could not be joined to CDISC data set
result
#> USUBJID Filename SampleID AGEGRP AGE18 STDDRS
#> 1 AB12345-CHN-1-id-307 eset 06520046C0018R 12 - <18 years < 18 DEATH
#> 2 AB12345-CHN-11-id-220 eset 06520105C0017R 12 - <18 years < 18
#> 3 AB12345-CHN-15-id-201 eset 06520103C0017R >= 18 years >= 18 DEATH
#> 4 AB12345-CHN-15-id-262 eset 06520067C0018R 2 - <6 years < 18
#> 5 AB12345-CHN-3-id-128 eset 06520011B0023R >= 18 years >= 18 DEATH
#> 6 AB12345-CHN-7-id-267 eset 06520092C0017R 12 - <18 years < 18 DEATH
#> 7 AB12345-NGA-11-id-173 eset 06520062C0017R 6 - <12 years < 18 DEATH
#> 8 AB12345-RUS-3-id-378 eset 06520063C0043R 12 - <18 years < 18 DEATH
#> 9 AB12345-USA-1-id-261 eset 06520022C0017R 12 - <18 years < 18
#> 10 AB12345-USA-1-id-45 eset 06520001B0023R >= 18 years >= 18 DEATH
#> STDDRSD STDSSDT TRTDRS
#> 1 DEATH DUE TO PROGRESSION OF DISEASE 07/24/2016 PROGRESSIVE DISEASE
#> 2 PROGRESSIVE DISEASE
#> 3 DEATH DUE TO PROGRESSION OF DISEASE 08/12/2016 PROGRESSIVE DISEASE
#> 4 PROGRESSIVE DISEASE
#> 5 DEATH DUE TO PROGRESSION OF DISEASE 05/31/2016 ADVERSE EVENT
#> 6 DEATH DUE TO PROGRESSION OF DISEASE 02/16/2017 PROGRESSIVE DISEASE
#> 7 DEATH DUE TO PROGRESSION OF DISEASE 09/11/2016 PROGRESSIVE DISEASE
#> 8 DEATH DUE TO PROGRESSION OF DISEASE 08/05/2016 PROGRESSIVE DISEASE
#> 9 PROGRESSIVE DISEASE
#> 10 DEATH DUE TO PROGRESSION OF DISEASE 01/08/2016 PROGRESSIVE DISEASE
#> TRTDRSD BHDCIRC BHDCIRCU ADAFL BLANP BKPS BLKS BTANNER
#> 1 PROGRESSION OF DISEASE NA Y NA 80 80 NA
#> 2 PROGRESSION OF DISEASE NA Y 100 NA 100 NA
#> 3 PROGRESSION OF DISEASE NA Y NA 90 90 NA
#> 4 PROGRESSION OF DISEASE NA Y NA 100 100 NA
#> 5 ADVERSE EVENT NA Y 100 NA 100 NA
#> 6 PROGRESSION OF DISEASE NA Y 100 NA 100 NA
#> 7 PROGRESSION OF DISEASE NA Y NA 100 100 NA
#> 8 PROGRESSION OF DISEASE NA Y 90 NA 90 NA
#> 9 PROGRESSION OF DISEASE NA Y NA 90 90 NA
#> 10 PROGRESSION OF DISEASE NA Y NA 90 90 NA
#> FRPST DURIDX DURSAF DURSUR LNTHRPY AENCIFL STUDYID
#> 1 POST-MENARCHAL 61.667351 1.6755647 5.158111 5 NA AB12345
#> 2 PRE-MENARCHAL 14.981520 3.0882957 5.815195 4 NA AB12345
#> 3 10.841889 0.9856263 3.055441 4 NA AB12345
#> 4 131.088296 1.6755647 19.252567 3 NA AB12345
#> 5 55.030801 0.9856263 5.026694 3 NA AB12345
#> 6 7.687885 3.0225873 12.418891 1 NA AB12345
#> 7 99.285421 3.5811088 6.340862 7 NA AB12345
#> 8 93.568789 0.9856263 4.665298 3 NA AB12345
#> 9 41.626283 1.6755647 18.858316 3 NA AB12345
#> 10 45.733060 0.6570842 2.299795 2 NA AB12345
#> RFSTDTC RFENDTC RFXSTDTC RFXENDTC
#> 1 2016-03-10T14:05 2016-03-31T15:49 2016-03-10T14:05 2016-03-31T15:49
#> 2 2017-04-11T12:35 2017-06-14T11:45 2017-04-11T12:35 2017-06-14T11:45
#> 3 2016-05-31T14:10 2016-05-31T14:10 2016-05-31T14:10 2016-05-31T14:10
#> 4 2016-01-11T14:30 2016-02-01T13:30 2016-01-11T14:30 2016-02-01T13:30
#> 5 2016-01-14T12:37 2016-01-14T12:37 2016-01-14T12:37 2016-01-14T12:37
#> 6 2016-02-12T11:05 2016-04-14T12:00 2016-02-12T11:05 2016-04-14T12:00
#> 7 2016-03-21T15:40 2016-06-08T18:00 2016-03-21T15:40 2016-06-08T18:00
#> 8 2016-03-24T14:25 2016-03-24T14:25 2016-03-24T14:25 2016-03-24T14:25
#> 9 2016-02-08T12:37 2016-02-29T14:15 2016-02-08T12:37 2016-02-29T14:15
#> 10 2015-11-05T11:00 2015-11-05T11:00 2015-11-05T11:00 2015-11-05T11:00
#> RFICDTC RFPENDTC DTHDTC DTHFL SITEID INVID AGE AGEU SEX
#> 1 2016-02-18 2016-07-24 2016-07-24 Y 283495 223804 12 YEARS F
#> 2 2017-04-03 283694 456732 15 YEARS M
#> 3 2016-05-11 2016-08-12 2016-08-12 Y 282087 468105 27 YEARS F
#> 4 2016-01-07 282087 468105 2 YEARS F
#> 5 2015-12-30 2016-05-31 2016-05-31 Y 283495 223804 19 YEARS F
#> 6 2016-02-04 2017-02-16 2017-02-16 Y 280959 20842 16 YEARS M
#> 7 2016-03-02 2016-09-11 2016-09-11 Y 283497 241874 7 YEARS F
#> 8 2016-03-16 2016-08-05 2016-08-05 Y 284024 457432 13 YEARS M
#> 9 2016-02-01 281049 457179 16 YEARS F
#> 10 2015-10-30 2016-01-08 2016-01-08 Y 283971 235545 19 YEARS F
#> RACE ETHNIC ARMCD ARM ACTARMCD
#> 1 WHITE NOT HISPANIC OR LATINO COH3 COHORT 3 COH3
#> 2 WHITE NOT HISPANIC OR LATINO COH12 COHORT 12 COH12
#> 3 UNKNOWN NOT REPORTED COH9E COHORT 9E COH9E
#> 4 UNKNOWN NOT REPORTED COH1 COHORT 1 COH1
#> 5 MULTIPLE NOT HISPANIC OR LATINO COH1 COHORT 1 COH1
#> 6 WHITE NOT HISPANIC OR LATINO COH9O COHORT 9O COH9O
#> 7 BLACK OR AFRICAN AMERICAN HISPANIC OR LATINO COH6 COHORT 6 COH6
#> 8 WHITE NOT HISPANIC OR LATINO COH8 COHORT 8 COH8
#> 9 ASIAN NOT HISPANIC OR LATINO COH1 COHORT 1 COH1
#> 10 UNKNOWN HISPANIC OR LATINO COH6 COHORT 6 COH6
#> ACTARM COUNTRY DMDTC DMDY BAGE BAGEU BWT BWTU BHT BHTU BBMI
#> 1 COHORT 3 CHN 2016-02-18 -21 12 YEARS 50.00 kg 157.0 cm 20.28480
#> 2 COHORT 12 CHN 2017-04-04 -7 15 YEARS 26.15 kg 136.0 cm 14.13819
#> 3 COHORT 9 CHN 2016-05-25 -6 27 YEARS 61.60 kg 173.0 cm 20.58204
#> 4 COHORT 1 CHN 2016-01-07 -4 2 YEARS 64.60 kg 177.1 cm 20.59659
#> 5 COHORT 1 CHN 2015-12-30 -15 19 YEARS 40.60 kg 154.0 cm 17.11924
#> 6 COHORT 9 CHN 2016-02-04 -8 16 YEARS 45.20 kg 161.1 cm 17.41596
#> 7 COHORT 6 NGA 2016-03-02 -19 7 YEARS 53.90 kg 176.0 cm 17.40057
#> 8 COHORT 8 RUS 2016-03-22 -2 13 YEARS 25.40 kg 125.0 cm 16.25600
#> 9 COHORT 1 USA 2016-02-01 -7 16 YEARS 104.70 kg 172.0 cm 35.39075
#> 10 COHORT 6 USA 2015-10-30 -6 19 YEARS 57.00 kg 172.0 cm 19.26717
#> ITTFL SAFFL INFCODT RANDDT TRTSDTC TRTSDTM
#> 1 Y Y 2016-02-18 2016-03-09 2016-03-10T14:05 2016-03-10 14:05:00
#> 2 Y Y 2017-04-03 2017-04-11 2017-04-11T12:35 2017-04-11 12:35:00
#> 3 Y Y 2016-05-11 2016-05-31 2016-05-31T14:10 2016-05-31 14:10:00
#> 4 Y Y 2016-01-07 2016-01-11 2016-01-11T14:30 2016-01-11 14:30:00
#> 5 Y Y 2015-12-30 2016-01-14 2016-01-14T12:37 2016-01-14 12:37:00
#> 6 Y Y 2016-02-04 2016-02-09 2016-02-12T11:05 2016-02-12 11:05:00
#> 7 Y Y 2016-03-02 2016-03-21 2016-03-21T15:40 2016-03-21 15:40:00
#> 8 Y Y 2016-03-16 2016-03-24 2016-03-24T14:25 2016-03-24 14:25:00
#> 9 Y Y 2016-02-01 2016-02-03 2016-02-08T12:37 2016-02-08 12:37:00
#> 10 Y Y 2015-10-30 2015-11-05 2015-11-05T11:00 2015-11-05 11:00:00
#> TRTSTMF TRTEDTM TRTETMF TRTDUR DISCSTUD DISCDEAT DISCAE DISTRTFL
#> 1 S 2016-03-31 16:55:59 S 22 Y Y N Y
#> 2 S 2017-06-14 12:15:59 S 65 N N N Y
#> 3 S 2016-05-31 15:10:59 S 1 Y Y N Y
#> 4 S 2016-02-01 14:30:59 S 22 N N N Y
#> 5 S 2016-01-14 13:37:59 S 1 Y Y N Y
#> 6 S 2016-04-14 12:30:59 S 63 Y Y N Y
#> 7 S 2016-06-08 18:30:59 S 80 Y Y N Y
#> 8 S 2016-03-24 15:30:59 S 1 Y Y N Y
#> 9 S 2016-02-29 14:48:59 S 22 N N N Y
#> 10 S 2015-11-05 12:00:59 S 1 Y Y N Y
#> AEWITHFL ALIVDT
#> 1 N 2016-07-24
#> 2 N 2017-09-27
#> 3 N 2016-08-12
#> 4 N 2017-08-15
#> 5 Y 2016-05-31
#> 6 N 2017-02-16
#> 7 N 2016-09-11
#> 8 N 2016-08-05
#> 9 N 2017-08-28
#> 10 N 2016-01-08
#> COHORT
#> 1 Cohort 3 (NEUROBLASTOMA)
#> 2 Cohort 12 (ATYPICAL TERATOID RHABOID TUMOR)
#> 3 Cohort 9 (OTHER TUMOR TYPES WITH DOCUMENTED PD-L1 EXPRESSION)
#> 4 Cohort 1 (EWING SARCOMA)
#> 5 Cohort 1 (EWING SARCOMA)
#> 6 Cohort 9 (OTHER TUMOR TYPES WITH DOCUMENTED PD-L1 EXPRESSION)
#> 7 Cohort 6 (OSTEOSARCOMA)
#> 8 Cohort 8 (WILMS TUMOR)
#> 9 Cohort 1 (EWING SARCOMA)
#> 10 Cohort 6 (OSTEOSARCOMA)
#> TTYPE
#> 1 NEUROBLASTOMA
#> 2 ATYPICAL TERATOID RHABDOID TUMOR
#> 3 GERM CELL TUMOR - YOLK SAC TUMOR (ENDODERMAL SINUS TUMOR) WITH DOCUMENTED PD-L1 EXPRESSION
#> 4 EWING SARCOMA
#> 5 EWING SARCOMA
#> 6 OTHER TUMOR TYPES WITH DOCUMENTED PD-L1 EXPRESSION ON EITHER TUMOR CELLS OR IMMUNE CELLS (TUMORS TYPE MUST NOT BE INCLUDED IN LIST ABOVE)
#> 7 OSTEOSARCOMA
#> 8 WILMS TUMOR
#> 9 EWING SARCOMA
#> 10 OSTEOSARCOMA
#> STDSSDY low_depth_flag tech_failure_flag GeneID.1820 extra
#> 1 137 FALSE FALSE 16 10
#> 2 NA FALSE FALSE 54 4
#> 3 74 FALSE FALSE 567 6
#> 4 NA FALSE FALSE 153 2
#> 5 139 FALSE FALSE 49 1
#> 6 371 FALSE FALSE 111 5
#> 7 175 TRUE FALSE 180 9
#> 8 135 TRUE FALSE 94 3
#> 9 NA FALSE FALSE 171 8
#> 10 65 FALSE FALSE 118 7