error report on estimating the heritability and genetic correlation

[Tong Gong]

Hi, 

I am quite new to LDSC and currently experience with an error while running the tutorial codes to estimate the heritability and genetic correlation. Could someone take a look at the log and let me know what the problem and possible solution could be?

I have successfully got the anaconda and python 2.7 under my working server. By following each step of the tutorial (https://github.com/bulik/ldsc/wiki/Heritability-and-Genetic-Correlation), I was able to download summary statistics data from pgc website etc. and munge the data. However, the codes for LD score regression and heritabiliy did not go through after reading the SNPs data (see below for the log file). 

*********************************************************************

* LD Score Regression (LDSC)

* Version 1.0.0

* (C) 2014-2015 Brendan Bulik-Sullivan and Hilary Finucane

* Broad Institute of MIT and Harvard / MIT Department of Mathematics

* GNU General Public License v3

*********************************************************************

Call: 

./ldsc.py \

--ref-ld-chr eur_w_ld_chr/ \

--out scz_bip \

--rg scz.sumstats.gz,bip.sumstats.gz \

--w-ld-chr eur_w_ld_chr/ 

Beginning analysis at Thu Jul 28 16:59:32 2016

Reading summary statistics from scz.sumstats.gz ...

Read summary statistics for 844500 SNPs.

Reading reference panel LD Score from eur_w_ld_chr/[1-22] ...

Traceback (most recent call last):

  File "./ldsc.py", line 626, in <module>

    sumstats.estimate_rg(args, log)

  File "/home/tongon/ldsc/ldscore/sumstats.py", line 330, in estimate_rg

    alleles=True, dropna=True)

  File "/home/tongon/ldsc/ldscore/sumstats.py", line 237, in _read_ld_sumstats

    ref_ld = _read_ref_ld(args, log)

  File "/home/tongon/ldsc/ldscore/sumstats.py", line 81, in _read_ref_ld

    'reference panel LD Score', ps.ldscore_fromlist)

  File "/home/tongon/ldsc/ldscore/sumstats.py", line 151, in _read_chr_split_files

    out = parsefunc(_splitp(chr_arg), _N_CHR, **kwargs)

  File "/home/tongon/ldsc/ldscore/parse.py", line 93, in ldscore_fromlist

    y = ldscore(fh, num)

  File "/home/tongon/ldsc/ldscore/parse.py", line 145, in ldscore

    x = x.sort_values(by=['CHR', 'BP']) # SEs will be wrong unless sorted

  File "/usr/local/anaconda/lib/python2.7/site-packages/pandas/core/generic.py", line 2150, in __getattr__

    (type(self).__name__, name))

AttributeError: 'DataFrame' object has no attribute 'sort_values'

Analysis finished at Thu Jul 28 16:59:38 2016

Total time elapsed: 6.16s

Does anyone know what the problem could have been? Many thanks in advance.

Best regards,

Tong 

Tong Gong | PhD 

Department of Medical Epidemiology and Biostatistics | Nobels väg 12A

Karolinska Institutet | 17 177 Stockholm

tong...@ki.se | +46 70 032 08 47 | ki.se

[Raymond Walters]

Hi Tong,

This error comes from having a older version of pandas. I believe the current requirement is version 0.17 or higher. Probably easiest to resolve by updating Anaconda (any Anaconda version 2.4.0 or later should work).

Cheers,

Raymond

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[Tong Gong]

Hi Raymond, 

Thanks very much for the quick check. I will update the Anaconda then.

Best, 
Tong