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 Request help for SAS programmer
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Posted on 01-03-14 1:15 PM     Reply [Subscribe]
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I have a bunch of text files to restructure for analysis in PLINK. Any SAS programmers in Sajha who can help to resolve this. To make this simple I have copied first 4 rows from 3 files and showed in the last 3 rows that the file I want to create. Please let me know if somebody is willing t help on this problem. I can e-mail the files. Thanks!!!!!

 

Filename: FileReport1.txt

#Source file: FinalReport1.csv

 

#Column header: SNP_id allele1_Forward allele2_Forward GenCall_score intensity1 intensity2

200006 T C 0.8190 1.253 1.110

200052 T T 0.9526 0.021 0.928

Filename: FileReport42.txt

#Source file: FinalReport42.csv

#Column header: SNP_id allele1_Forward allele2_Forward GenCall_score intensity1 intensity2

200006 T C 0.8190 1.049 1.004

200052 T T 0.9526 0.019 0.928

Filename: FileReport53.txt

#Source file: FinalReport53.csv

#Column header: SNP_id allele1_Forward allele2_Forward GenCall_score intensity1 intensity2

200006 C C 0.8190 0.043 1.637

200052 A T 0.9526 0.690 0.691

 

Restructured data into a file like below:

SNP_id A1_1 A2_1 A1_42 A2_42 A1_53 A2_53

200006 T C T C C C

200052 T T T T A T


 
Posted on 01-03-14 3:10 PM     [Snapshot: 53]     Reply [Subscribe]
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Import the table from the CSV or txt file and create the following three tables.
test1 a,
     test42b,
     test53 c

and then join it.

Hope this one works.
PROC SQL;

create table test as

select

 a.SNP_id
,a.allele1_Forward as a1_1
,a.allele2_Forward as a2_1
,b.allele1_Forward as a1_42
,b.allele2_Forward as a2_42
,c.allele1_Forward as a1_53
,c.allele2_Forward as a2_53

from test1 a,
     test42b,
     test53 c

where a.snp_id=b.snp_id and b.snp_id=c.snp_id;
quit;

proc print data=test;
run;


 
Posted on 01-03-14 3:25 PM     [Snapshot: 60]     Reply [Subscribe]
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You can use PROC SQL
or rename each variables in the dataset.

For example: 
for data one (rename =allele1_Forward =A1_1  allele2_Forward= A1_42.........)
For data two (rename = allele1_Forward = A2_1 allele2_Forward = A2_43 ......)
do the same thing for data three

Then at the end, Merge 3 dataset by SNP_ID

Hope that helps.

 
Posted on 01-04-14 9:37 AM     [Snapshot: 208]     Reply [Subscribe]
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Nothing against sas, do you use R? I personnally prefer R for data manipulation and graphs
 


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