About MajaFerencakovic

MajaFerencakovic · ‎10-13-2016

Works!!! Thank you! It is nice to have so many working solutions.

MajaFerencakovic · ‎10-13-2016

This one is also correct! I really hope this will help people doing genetics to prepare data for outdated softwares and programers who don't understand that they really should start to work on improvements of their procedures because we are getting more and more data everyday

MajaFerencakovic · ‎10-13-2016

This one works perfectly! Thanks!

MajaFerencakovic · ‎10-12-2016

the file by itself is fine. All headers are in but data starts in the same line as headers

MajaFerencakovic · ‎10-12-2016

hm... still not working... 😞

MajaFerencakovic · ‎10-12-2016

looks promising. I tried it on smaller data set (40000). But, after the last one header (snp40000), data starts to apear in the same line.

MajaFerencakovic · ‎10-12-2016

guys, this is not helpful. This is standard .ped format used in genetics. So can we skip the part why would I need to have 2000000 variables. I have them, I must deal with them...

MajaFerencakovic · ‎10-12-2016

well, here it is not usefull to discuss why my colegue need wide instead of long format. I have them in long. But as I said it, this is not up to me... However those are genotype data, lot of info... This is kind of standard format. TextPad opens this one nicely. No issues at all. If issues would apear I woul use long file text viewer or something to check. As I said, data are fine. Only header stops. No problem with exporting data. But guy needs header to...

MajaFerencakovic · ‎10-12-2016

Dear friends I need your help again. I have data set with more than 2000000 variables id snp1 snp2 snp3 ... snp2000000 i want to export it to any kind of delimited file, and preserve header. I tried few stuff like: PROC EXPORT DATA= bikovi (OBS=0) OUTFILE= "C:\Users\Maja\Desktop\gv50.csv" DBMS=CSV REPLACE; PUTNAMES=YES; RUN; DATA _NULL_; SET bikovi; FILE "C:\Users\Maja\Desktop\gv50.csv" MOD DSD DLM=',' LRECL=5000000 ; PUT (_ALL_) (:) ; RUN; and while the data are fine, my header is stopping at snp3708 every time. What can be a reason? I tried on smaller data set (40000 variables) and the story was the same. My data are very simple id is character value length 15 but if needed i can have it as numeric 1,2,3...671 while SNPs are numbers 0,1,2. I tried also a robust macro from http://support.sas.com/kb/24/727.html but this one only complicated everything Hope you guys can help me Thanks!

MajaFerencakovic · ‎06-19-2016

It works nice on 10 variables example. I will now try to run the real thing

MajaFerencakovic · ‎06-19-2016

thanks for the tip. Well It looks like I missed one zero. It is 600000 at the beginning.

MajaFerencakovic · ‎06-19-2016

I will give it a try and let you know

MajaFerencakovic · ‎06-19-2016

Dear friends, I need your help with my problem. I have genotype data set loking like this animal_id;snp_1;snp_2;snp3 ... snp_600000 animal1;0;2;1...2 animal2;1;2;0...0 i should recode values under snp_1...snp_600000 that are now 0, 1 or 2 to AA, AB, BB and this is not an issue, but then I have to export txt file which would look like this animal1;A;A;B;B;A;B...B;B animal2;A;B;B;B;A;A...A;A in other words from 600000 variables per animal i must get 1200000 (i know it is big...) i guess that two arrays would fix a problem, but my files are huge and more elegant solution would be nice. Thanks Example of input and desirable output is attached

MajaFerencakovic · ‎09-23-2015

Yes! Thank you! I was not aware that I did not change the &i to &item. This works great

MajaFerencakovic · ‎09-23-2015

Ok, this works partly. For example I did this and for first two was ok %macro do_over(list); %local i item ; %do i=1 %to %sysfunc(countw(&list)); %let item=%scan(&list,&i); data file_&i (drop = snp1 snp2 bp_position1 bp_position2 fid pheno nsnp gustp phom phet) ; length bull_id $15. snp1 $50. snp2 $50. bp_position1 $12. bp_position2 $12.; infile "C:\Users\Maja Zmaja\Desktop\ASD2015\Btauroh_&i" delimiter=" " firstobs=2; input fid $ bull_id $ pheno $ chr snp1 $ snp2 $ bp_position1 $ bp_position2 $ kilobaza nsnp gustp phom phet @@; run; %end; %mend do_over; %do_over(1 2 8); But then I got this ERROR: Physical file does not exist, C:\Users\Maja Zmaja\Desktop\ASD2015\Btauroh_3. And what ever combination I put in list I get the same result. I tried %do_over(4 8); and still obtained data from Btauroh_1 and Btauroh_2 and that was it

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Re: Export 2000000 variables into delimited file

Re: Export 2000000 variables into delimited file

Re: Export 2000000 variables into delimited file

Re: Export 2000000 variables into delimited file

Re: Export 2000000 variables into delimited file

Re: Export 2000000 variables into delimited file

Re: Export 2000000 variables into delimited file

Re: Export 2000000 variables into delimited file

Export 2000000 variables into delimited file

Re: recode genotypes 0, 1, 2 to space delimited SNPs A A A B B B

Re: Export 2000000 variables into delimited file

Re: Export 2000000 variables into delimited file

How to fill up the range

Re: Export 2000000 variables into delimited file

Re: Export 2000000 variables into delimited file

Re: Export 2000000 variables into delimited file

Re: Export 2000000 variables into delimited file

Re: Export 2000000 variables into delimited file

Re: Export 2000000 variables into delimited file

Re: Export 2000000 variables into delimited file

Re: Export 2000000 variables into delimited file

Export 2000000 variables into delimited file

Re: recode genotypes 0, 1, 2 to space delimited SNPs A A A B B B

Re: recode genotypes 0, 1, 2 to space delimited SNPs A A A B B B

Re: recode genotypes 0, 1, 2 to space delimited SNPs A A A B B B

recode genotypes 0, 1, 2 to space delimited SNPs A A A B B B

Re: Macro for importing multiple txt files with nonsequential names

Re: Macro for importing multiple txt files with nonsequential names