![[Experimental]](figures/lifecycle-experimental.svg)
This is a useful function when trying to join genetic with CDISC data sets.
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.
Value
A data.frame which contains columns from both data sets merged by the keys.
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