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bulik / ldsc

LD Score Regression (LDSC)
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Can't find munge_sumstats.py script #23

Closed r03ert0 closed 9 years ago

r03ert0 commented 9 years ago

Hello,

Thank you for making ldsc available !

I'm trying to do the LD score tutorial from the wiki, I downloaded the PGC bip and scz files, but I can't find the script munge_sumstats.py. I tried with the script ldsc/ldscore/sumstats.py instead, it produced two .pyc files, but no results. This is the command I used: python sumstats.py --sumstats $datadir/pgc.cross.scz/pgc.cross.SCZ17.2013-05.txt --N 17115 --out scz

best, roberto

bulik commented 9 years ago

Hi Roberto,

The (half-written) documentation refers to the dev branch (which will soon become v1.0.0). You can switch to the dev branch with

git checkout dev

On Tue, Feb 10, 2015 at 10:14 AM, Roberto Toro notifications@github.com wrote:

Hello,

Thank you for making ldsc available !

I'm trying to do the LD score tutorial from the wiki, I downloaded the PGC bip and scz files, but I can't find the script munge_sumstats.py. I tried with the script ldsc/ldscore/sumstats.py instead, it produced two .pyc files, but no results. This is the command I used: python sumstats.py --sumstats $datadir/pgc.cross.scz/pgc.cross.SCZ17.2013-05.txt --N 17115 --out scz

best, roberto

— Reply to this email directly or view it on GitHub https://github.com/bulik/ldsc/issues/23.

r03ert0 commented 9 years ago

Thank you Brendan ! Where can I find the files for the --ref-ld-chr switch ? I downloaded the 1k_eur_r2_hm3snps_se_weights.RDS file from the ftp link in your Nature Genetics paper, but it doesn't seem to be the right file...

best, roberto

bulik commented 9 years ago

Correct, that's not the right file (I told NG to remove that link in the proofs ... annoying).

I'm still working on putting the tutorial together (as evidenced by $URL_GOES_HERE), but I've just put up some LD Scores that you can download. These are suitable for European-ancestry GWAS data, including the two psychiatric datasets used in the genetic correlation tutorial.

http://www.broadinstitute.org/~bulik/eur_ldscores/

On Tue, Feb 10, 2015 at 11:09 AM, Roberto Toro notifications@github.com wrote:

Thank you Brendan !

and the files for the --ref-ld-chr switch ? I downloaded the 1k_eur_r2_hm3snps_se_weights.RDS file from the ftp link in your Nature Genetics paper, but it doesn't seem to be the right file...

best, roberto

On Tue, Feb 10, 2015 at 4:16 PM, Brendan Bulik-Sullivan < notifications@github.com> wrote:

Hi Roberto,

The (half-written) documentation refers to the dev branch (which will soon become v1.0.0). You can switch to the dev branch with

git checkout dev

On Tue, Feb 10, 2015 at 10:14 AM, Roberto Toro <notifications@github.com

wrote:

Hello,

Thank you for making ldsc available !

I'm trying to do the LD score tutorial from the wiki, I downloaded the PGC bip and scz files, but I can't find the script munge_sumstats.py. I tried with the script ldsc/ldscore/sumstats.py instead, it produced two .pyc files, but no results. This is the command I used: python sumstats.py --sumstats $datadir/pgc.cross.scz/pgc.cross.SCZ17.2013-05.txt --N 17115 --out scz

best, roberto

— Reply to this email directly or view it on GitHub https://github.com/bulik/ldsc/issues/23.

— Reply to this email directly or view it on GitHub https://github.com/bulik/ldsc/issues/23#issuecomment-73715909.

— Reply to this email directly or view it on GitHub https://github.com/bulik/ldsc/issues/23#issuecomment-73727140.

r03ert0 commented 9 years ago

great! everything works now :) thank you!