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
beta · Jan 3, 2014 1:15 PM · 16,320 views
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;
DEVN · Jan 3, 2014 3:10 PM
You can use PROC SQLor 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.
I485 · Jan 3, 2014 3:25 PM
Nothing against sas, do you use R? I personnally prefer R for data manipulation and graphs
shivanagar · Jan 4, 2014 9:37 AM
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