topic Re: Merging by Text in SAS Programming

Merging by Text

newsas007 — Wed, 23 Dec 2020 02:23:18 GMT

Hi all,

I had asked a similar question a while ago but I am running into some issues.

Dataset A contains information on the gene type and list of prescribed drugs associated with it. For example, the prescribed drugs for Gene type ‘a’ are as follows: Afatinib,Neo-Cetuximab,Dacomitinib,Erlotinib,Gefitinib,Lapatinib,Necitumumab,Osimertinib,Panitumumab.

The dataset B contains information on what the patient got prescribed and the dates associated with it. For example, ID#1 got Panitumumab, Binimetinib, and Neo-Cetuximab on different dates.

Therefore, in my merged dataset, I would like to get a row for Panitumimab and a row for Neo-Cetuximab. Further, in case the patient got a drug that is not listed in the drug_list I want it to be missing. For example, ID #6 prescribed drug Idelalisib does not match the drug_list for the specific gene ‘b’. Similar scenario for and ID#7

Here are the datasets and the code I had started using.

data A;
informat id 3. date_a mmddyy10. Gene_type $3. Drug_list $200.;
input id date_a Gene_type Drug_list;
format id 3. date_a mmddyy10. Gene_Type$3. Drug_list $200.;
cards;
1 1/2/2018 a Afatinib,Neo-Cetuximab,Dacomitinib,Erlotinib,Gefitinib,Lapatinib,Necitumumab,Osimertinib,Panitumumab
1 2/10/2019 b Cetuximab,Xanitumumab
2 3/3/2019 c Binimetinib,Cetuximab,Cobimetinib,Idelalisib,Panitumumab,Trametinib
3 1/2/2018 d Alpelisib,Everolimus,Temsirolimus
4 2/2/2019 f Ado-trastuzumab,Afatinib,Dacomitinib,Lapatinib,Neratinib,Pertuzumab,Trastuzumab,Trastuzumab-anns,Trastuzumab-dkst,Trastuzumab-dttb,Trastuzumab-pkrb,Trastuzumab-qyyp
4 2/10/2019 e Bosutinib,Dasatinib,Everolimus,Temsirolimus
5 3/3/2019 a Afatinib,Neo-Cetuximab,Dacomitinib,Erlotinib,Gefitinib,Lapatinib,Necitumumab,Osimertinib,Panitumumab
6 1/2/2018 c Binimetinib,Cetuximab,Cobimetinib,Idelalisib,Panitumumab,Trametinib
6 2/2/2019 b Cetuximab,Xanitumumab
7 2/10/2019 d Alpelisib,Everolimus,Temsirolimus
7 3/10/2019 b Cetuximab,Xanitumumab
;;;
proc sort; by id; run;

data B;
informat id 3. date_b mmddyy10. Drug $20.;
input id date_b Drug;
format id 3. date_b mmddyy10. Drug $200.;
cards;
1 2/01/2018 Panitumumab
1 3/02/2019 Binimetinib
1 3/28/2019 Neo-Cetuximab
2 3/23/2019 Trametinib
2 3/25/2019 Temsirolimus
3 2/01/2018 Alpelisib
5 3/21/2019 Dacomitinib
4 3/01/2019 Everolimus
4 4/01/2019 Cobimetinib
4 5/01/2019 Ado-trastuzumab
6 1/17/2018 Idelalisib
7 3/02/2019 Temsirolimus
7 4/01/2019 Binimetinib
;;;

Data Want:

ID	Date_a	Gene_type	Drug_list	Drug	Date_b
1	1/2/2018	a	Afatinib,Neo-Cetuximab,Dacomitinib,Erlotinib,Gefitinib,Lapatinib,Necitumumab,Osimertinib,Panitumumab	Panitumumab	2/1/2018
1	1/2/2018	a	Afatinib,Neo-Cetuximab,Dacomitinib,Erlotinib,Gefitinib,Lapatinib,Necitumumab,Osimertinib,Panitumumab	Neo-Cetuximab	3/28/2019
1	2/10/2019	b	Cetuximab,Xanitumumab
2	3/3/2019	c	Binimetinib,Cetuximab,Cobimetinib,Idelalisib,Panitumumab,Trametinib	Trametinib	3/23/2019
3	1/2/2018	d	Alpelisib,Everolimus,Temsirolimus	Alpelisib	2/1/2018
4	2/2/2019	f	Ado-trastuzumab,Afatinib,Dacomitinib,Lapatinib,Neratinib,Pertuzumab,Trastuzumab,Trastuzumab-anns,Trastuzumab-dkst,Trastuzumab-dttb	Ado-trastuzumab	5/1/2019
4	2/10/2019	e	Bosutinib,Dasatinib,Everolimus,Temsirolimus	Everolimus	3/1/2019
5	3/3/2019	a	Afatinib,Neo-Cetuximab,Dacomitinib,Erlotinib,Gefitinib,Lapatinib,Necitumumab,Osimertinib,Panitumumab	Dacomitinib	3/21/2019
6	1/2/2018	c	Binimetinib,Cetuximab,Cobimetinib,Idelalisib,Panitumumab,Trametinib	Idelalisib	1/17/2018
6	2/2/2019	b	Cetuximab,Xanitumumab
7	2/10/2019	d	Alpelisib,Everolimus,Temsirolimus	Temsirolimus	3/2/2019
7	3/10/2019	b	Cetuximab,Xanitumumab

Proc sql;
Create table c2 as select a.*, b.Drug,b.Date_b
from a a join b b on a.id=b.id
and findw( a.drug_list,strip(b.drug),',') > 0 and (b.date_b);
Quit;

Re: Merging by Text

ChrisNZ — Wed, 23 Dec 2020 02:18:48 GMT

so Neo-Cetuximab matches with Cetuximab?

Re: Merging by Text

newsas007 — Wed, 23 Dec 2020 02:24:44 GMT

@ChrisNZ: they are unique and different. For example #ID 1 only got Neo-Cetuximab.

Re: Merging by Text

ChrisNZ — Wed, 23 Dec 2020 02:36:54 GMT

1. Please format your code and your data

2. Something like this is what you need. Please alter to suit:

proc sql;
  create table WANT as 
  select GENES.*, DRUGS.DRUG, DRUGS.DATE_B
  from GENES join DRUGS 
    on GENES.ID=DRUGS.ID
   and findw( GENES.DRUG_LIST, prxchange('s/\A(Ado|Neo)-//',1,DRUGS.DRUG), ',- ', 't') 
 order by GENES.ID, GENE_TYPE ;
quit;

ID	DATE_A	GENE_TYPE	DRUG_LIST	DRUG	DATE_B
1	01/02/2018	a	Afatinib,Neo-Cetuximab,Dacomitinib,Erlotinib,Gefitinib,Lapatinib,Necitumumab,Osimertinib,Panitumumab	Neo-Cetuximab	03/28/2019
1	01/02/2018	a	Afatinib,Neo-Cetuximab,Dacomitinib,Erlotinib,Gefitinib,Lapatinib,Necitumumab,Osimertinib,Panitumumab	Panitumumab	02/01/2018
1	02/10/2019	b	Cetuximab,Xanitumumab	Neo-Cetuximab	03/28/2019
2	03/03/2019	c	Binimetinib,Cetuximab,Cobimetinib,Idelalisib,Panitumumab,Trametinib	Trametinib	03/23/2019
3	01/02/2018	d	Alpelisib,Everolimus,Temsirolimus	Alpelisib	02/01/2018
4	02/10/2019	e	Bosutinib,Dasatinib,Everolimus,Temsirolimus	Everolimus	03/01/2019
4	02/02/2019	f	Ado-trastuzumab,Afatinib,Dacomitinib,Lapatinib,Neratinib,Pertuzumab,Trastuzumab,Trastuzumab-anns,Trastuzumab-dkst,Trastuzumab-dttb,Trastuzumab-pkrb,Trastuzumab-qyyp	Ado-trastuzumab	05/01/2019
5	03/03/2019	a	Afatinib,Neo-Cetuximab,Dacomitinib,Erlotinib,Gefitinib,Lapatinib,Necitumumab,Osimertinib,Panitumumab	Dacomitinib	03/21/2019
6	01/02/2018	c	Binimetinib,Cetuximab,Cobimetinib,Idelalisib,Panitumumab,Trametinib	Idelalisib	01/17/2018
7	02/10/2019	d	Alpelisib,Everolimus,Temsirolimus	Temsirolimus	03/02/2019

Re: Merging by Text

ChrisNZ — Wed, 23 Dec 2020 02:42:16 GMT

> They are unique and different.

OK just replace

findw( GENES.DRUG_LIST, prxchange('s/\A(Ado|Neo)-//',1,DRUGS.DRUG), ',- ', 't')

with

findw( GENES.DRUG_LIST, DRUGS.DRUG), ', ', 't')

then, and report.

Re: Merging by Text

newsas007 — Wed, 23 Dec 2020 03:30:08 GMT

Thanks for this:
I used this code and got the output for ID#1 shows Neo-Cetuximab merging with Cetuximab. It should be a empty cell for drug and date_b because #ID1 was never given Cetuximab.
Basically, each drug name is unique. Neo-Cetuximab is different from Cetuximab and so does any drug with Ado- or any other prefix.I know it's probably a subtle change in the code. I am still trying..thanks again
proc sql;
create table WANT as
select GENES.*, DRUGS.DRUG, DRUGS.DATE_B
from GENES left join DRUGS
on GENES.ID=DRUGS.ID
and findw( GENES.DRUG_LIST, prxchange('s/\A(Ado|Neo)-//',1,DRUGS.DRUG), ',- ', 't')
order by GENES.ID, GENE_TYPE ;
quit;

Re: Merging by Text

ChrisNZ — Wed, 23 Dec 2020 03:41:27 GMT

Please format your code and data.

Re: Merging by Text

ChrisNZ — Wed, 23 Dec 2020 03:53:29 GMT

proc sql;
  select GENES.*, DRUGS.DRUG, DRUGS.DATE_B
  from GENES left join DRUGS 
    on GENES.ID=DRUGS.ID
   and findw( GENES.DRUG_LIST, DRUGS.DRUG, ',- ', 't') 
 order by GENES.ID, GENE_TYPE ;
quit;

ID	DATE_A	GENE_TYPE	DRUG_LIST	DRUG	DATE_B
1	01/02/2018	a	Afatinib,Neo-Cetuximab,Dacomitinib,Erlotinib,Gefitinib,Lapatinib,Necitumumab,Osimertinib,Panitumumab	Neo-Cetuximab	03/28/2019
1	01/02/2018	a	Afatinib,Neo-Cetuximab,Dacomitinib,Erlotinib,Gefitinib,Lapatinib,Necitumumab,Osimertinib,Panitumumab	Panitumumab	02/01/2018
1	02/10/2019	b	Cetuximab,Xanitumumab		.
2	03/03/2019	c	Binimetinib,Cetuximab,Cobimetinib,Idelalisib,Panitumumab,Trametinib	Trametinib	03/23/2019
3	01/02/2018	d	Alpelisib,Everolimus,Temsirolimus	Alpelisib	02/01/2018
4	02/10/2019	e	Bosutinib,Dasatinib,Everolimus,Temsirolimus	Everolimus	03/01/2019
4	02/02/2019	f	Ado-trastuzumab,Afatinib,Dacomitinib,Lapatinib,Neratinib,Pertuzumab,Trastuzumab,Trastuzumab-anns,Trastuzumab-dkst,Trastuzumab-dttb,Trastuzumab-pkrb,Trastuzumab-qyyp	Ado-trastuzumab	05/01/2019
5	03/03/2019	a	Afatinib,Neo-Cetuximab,Dacomitinib,Erlotinib,Gefitinib,Lapatinib,Necitumumab,Osimertinib,Panitumumab	Dacomitinib	03/21/2019
6	02/02/2019	b	Cetuximab,Xanitumumab		.
6	01/02/2018	c	Binimetinib,Cetuximab,Cobimetinib,Idelalisib,Panitumumab,Trametinib	Idelalisib	01/17/2018
7	03/10/2019	b	Cetuximab,Xanitumumab		.
7	02/10/2019	d	Alpelisib,Everolimus,Temsirolimus	Temsirolimus	03/02/2019

Re: Merging by Text

newsas007 — Wed, 23 Dec 2020 04:04:59 GMT

@ChrisNZ: Thank you so much for this! This works just fine. I am still learning subtle things 🙂
Thanks again.

Re: Merging by Text

ChrisNZ — Wed, 23 Dec 2020 04:07:38 GMT

Maybe remove the dash as a separator in the findw() function.

And don't forget to format and reread your question if you want to be helped.