Code Monkey home page Code Monkey logo

leap's People

Contributors

cwidmer avatar omerwe avatar

Stargazers

avatar avatar avatar avatar avatar avatar avatar avatar avatar

Watchers

avatar avatar avatar avatar avatar

Forkers

bioinformaticsarchive python3pkg joannavonberg dianacornejo

leap's Issues

h2>1

hello,
I've been recently using LEAP on two data sets on which it seems to have run without problems. I'm now trying it on a third data set but on this one I get h2 values >1 (as per below log). This consequently generates problems when I run probit.py:

/home/manduchi/mypy/lib/python2.7/site-packages/leap/probit.py:57: RuntimeWarning: invalid value encountered in sqrt
normPDF = stats.norm(0, np.sqrt(1-h2))
...

Can you advice?
Thanks,
Elisabetta

=== calc_h2.py run
python calc_h2.py --bfilesim data_autosome --prev 0.1 --pheno leap.phe --eigen leap_noChr1.kin.npz --extractSim noChr1.snps --related leap.rm
/home/
manduchi/mypy/lib/python2.7/site-packages/pysnptools/snpreader/bed.py:42: FutureWarning: 'count_A1' was not set. For now it will default to 'False', but in the future it will default to 'True'
warnings.warn("'count_A1' was not set. For now it will default to 'False', but in the future it will default to 'True'", FutureWarning)
WARNING:root:loadPhen is using default missing value of '-9'.
WARNING:root:loadPhen is using default missing value of '-9'.
29 individuals will be removed due to high relatedness
Removing the top 10 PCs from the kinship matrix
Computing h2 for a binary phenotype
h2: 1.241879

LEAP installation error

Hello LEAP developers,
I'm trying to install LEAP to be able to run Fast-LMM using binary traits for interaction analysis. However, I'm having a hard time installing LEAP. Any help is appreciated!

DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
Requirement already satisfied: leap_gwas in /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages/leap_gwas-0.1.7.2-py2.7.egg (0.1.7.2)
Requirement already satisfied: numpy in /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages (from leap_gwas) (1.16.6)
Requirement already satisfied: scipy in /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages (from leap_gwas) (1.2.3)
Collecting fastlmm
  Using cached https://files.pythonhosted.org/packages/4e/62/6bd368f9f7b7b3d2cc3d184c7f2f97d509a8402bb80dd51f135d1dc98857/fastlmm-0.4.8.tar.gz
  Installing build dependencies ... done
  WARNING: Missing build requirements in pyproject.toml for fastlmm from https://files.pythonhosted.org/packages/4e/62/6bd368f9f7b7b3d2cc3d184c7f2f97d509a8402bb80dd51f135d1dc98857/fastlmm-0.4.8.tar.gz#sha256=a3fb5c0468fb2978543d606d651292684943dd0fe66c975634ea17ea861823f1 (from leap_gwas).
  WARNING: The project does not specify a build backend, and pip cannot fall back to setuptools without 'wheel'.
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
    Preparing wheel metadata ... done
Requirement already satisfied: scikit-learn in /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages (from leap_gwas) (0.20.4)
Requirement already satisfied: pandas in /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages (from leap_gwas) (0.24.2)
Collecting statsmodels>=0.10.1
  Using cached https://files.pythonhosted.org/packages/53/1c/b83f6a4632b502a20b0f83bc5c25ebfa03eebd00efe9b45fcdcde1a0ab40/statsmodels-0.11.0.tar.gz
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
    Preparing wheel metadata ... done
Collecting psutil>=5.6.7
  Using cached https://files.pythonhosted.org/packages/aa/3e/d18f2c04cf2b528e18515999b0c8e698c136db78f62df34eee89cee205f1/psutil-5.7.2.tar.gz
Collecting matplotlib>=1.5.1
  Using cached https://files.pythonhosted.org/packages/9d/40/5ba7d4a3f80d39d409f21899972596bf62c8606f1406a825029649eaa439/matplotlib-2.2.5-cp27-cp27mu-manylinux1_x86_64.whl
Collecting pysnptools>=0.4.10
  Using cached https://files.pythonhosted.org/packages/29/6e/430a65ae359c52571878f045b481693f30c151302e410480fece8f62db25/pysnptools-0.4.20.tar.gz
  Installing build dependencies ... done
  WARNING: Missing build requirements in pyproject.toml for pysnptools>=0.4.10 from https://files.pythonhosted.org/packages/29/6e/430a65ae359c52571878f045b481693f30c151302e410480fece8f62db25/pysnptools-0.4.20.tar.gz#sha256=f1d007e02d3581e558f35a2bd53ed92cd9678d5326afb463f12047b9b26516c2 (from fastlmm->leap_gwas).
  WARNING: The project does not specify a build backend, and pip cannot fall back to setuptools without 'wheel'.
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
    Preparing wheel metadata ... done
Collecting dill>=0.2.9
  Using cached https://files.pythonhosted.org/packages/e2/96/518a8ea959a734b70d2e95fef98bcbfdc7adad1c1e5f5dd9148c835205a5/dill-0.3.2.zip
Requirement already satisfied: pytz>=2011k in /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages (from pandas->leap_gwas) (2020.1)
Requirement already satisfied: python-dateutil>=2.5.0 in /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages (from pandas->leap_gwas) (2.8.1)
Collecting patsy>=0.5
  Using cached https://files.pythonhosted.org/packages/ea/0c/5f61f1a3d4385d6bf83b83ea495068857ff8dfb89e74824c6e9eb63286d8/patsy-0.5.1-py2.py3-none-any.whl
Collecting subprocess32
  Using cached https://files.pythonhosted.org/packages/93/dc/3a0ae313f1cf0f59b582e8e14891196e51fca5db193558b7661bd32b8801/subprocess32-3.5.4-cp27-cp27mu-manylinux2014_x86_64.whl
Collecting cycler>=0.10
  Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Requirement already satisfied: six>=1.10 in /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages (from matplotlib>=1.5.1->fastlmm->leap_gwas) (1.15.0)
Collecting backports.functools-lru-cache
  Using cached https://files.pythonhosted.org/packages/da/d1/080d2bb13773803648281a49e3918f65b31b7beebf009887a529357fd44a/backports.functools_lru_cache-1.6.1-py2.py3-none-any.whl
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1
  Using cached https://files.pythonhosted.org/packages/8a/bb/488841f56197b13700afd5658fc279a2025a39e22449b7cf29864669b15d/pyparsing-2.4.7-py2.py3-none-any.whl
Collecting kiwisolver>=1.0.1
  Using cached https://files.pythonhosted.org/packages/3d/78/cb9248b2289ec31e301137cedbe4ca503a74ca87f88cdbfd2f8be52323bf/kiwisolver-1.1.0-cp27-cp27mu-manylinux1_x86_64.whl
Collecting h5py>=2.10.0
  Using cached https://files.pythonhosted.org/packages/12/90/3216b8f6d69905a320352a9ca6802a8e39fdb1cd93133c3d4163db8d5f19/h5py-2.10.0-cp27-cp27mu-manylinux1_x86_64.whl
Collecting bgen-reader>=4.0.4
  Using cached https://files.pythonhosted.org/packages/ef/f4/2775ad723b7011603ea1a3ca7021a554465e3175eaa1499590b11960fce7/bgen-reader-4.0.6.tar.gz
  Installing build dependencies ... error
  ERROR: Command errored out with exit status 1:
   command: /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/bin/python /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-x8e5wp/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- 'setuptools>=49.3.0' 'wheel>=0.34.2'
       cwd: None
  Complete output (3 lines):
  DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
  ERROR: Could not find a version that satisfies the requirement setuptools>=49.3.0 (from versions: 0.6b1, 0.6b2, 0.6b3, 0.6b4, 0.6rc1, 0.6rc2, 0.6rc3, 0.6rc4, 0.6rc5, 0.6rc6, 0.6rc7, 0.6rc8, 0.6rc9, 0.6rc10, 0.6rc11, 0.7.2, 0.7.3, 0.7.4, 0.7.5, 0.7.6, 0.7.7, 0.7.8, 0.8, 0.9, 0.9.1, 0.9.2, 0.9.3, 0.9.4, 0.9.5, 0.9.6, 0.9.7, 0.9.8, 1.0, 1.1, 1.1.1, 1.1.2, 1.1.3, 1.1.4, 1.1.5, 1.1.6, 1.1.7, 1.2, 1.3, 1.3.1, 1.3.2, 1.4, 1.4.1, 1.4.2, 2.0, 2.0.1, 2.0.2, 2.1, 2.1.1, 2.1.2, 2.2, 3.0, 3.0.1, 3.0.2, 3.1, 3.2, 3.3, 3.4, 3.4.1, 3.4.2, 3.4.3, 3.4.4, 3.5, 3.5.1, 3.5.2, 3.6, 3.7, 3.7.1, 3.8, 3.8.1, 4.0, 4.0.1, 5.0, 5.0.1, 5.0.2, 5.1, 5.2, 5.3, 5.4, 5.4.1, 5.4.2, 5.5, 5.5.1, 5.6, 5.7, 5.8, 6.0.1, 6.0.2, 6.1, 7.0, 8.0, 8.0.1, 8.0.2, 8.0.3, 8.0.4, 8.1, 8.2, 8.2.1, 8.3, 9.0, 9.0.1, 9.1, 10.0, 10.0.1, 10.1, 10.2, 10.2.1, 11.0, 11.1, 11.2, 11.3, 11.3.1, 12.0, 12.0.1, 12.0.2, 12.0.3, 12.0.4, 12.0.5, 12.1, 12.2, 12.3, 12.4, 13.0.1, 13.0.2, 14.0, 14.1, 14.1.1, 14.2, 14.3, 14.3.1, 15.0, 15.1, 15.2, 16.0, 17.0, 17.1, 17.1.1, 18.0, 18.0.1, 18.1, 18.2, 18.3, 18.3.1, 18.3.2, 18.4, 18.5, 18.6, 18.6.1, 18.7, 18.7.1, 18.8, 18.8.1, 19.0, 19.1, 19.1.1, 19.2, 19.3, 19.4, 19.4.1, 19.5, 19.6, 19.6.1, 19.6.2, 19.7, 20.0, 20.1, 20.1.1, 20.2.2, 20.3, 20.3.1, 20.4, 20.6.6, 20.6.7, 20.6.8, 20.7.0, 20.8.0, 20.8.1, 20.9.0, 20.10.1, 21.0.0, 21.1.0, 21.2.0, 21.2.1, 21.2.2, 22.0.0, 22.0.1, 22.0.2, 22.0.4, 22.0.5, 23.0.0, 23.1.0, 23.2.0, 23.2.1, 24.0.0, 24.0.1, 24.0.2, 24.0.3, 24.1.0, 24.1.1, 24.2.0, 24.2.1, 24.3.0, 24.3.1, 25.0.0, 25.0.1, 25.0.2, 25.1.0, 25.1.1, 25.1.2, 25.1.3, 25.1.4, 25.1.5, 25.1.6, 25.2.0, 25.3.0, 25.4.0, 26.0.0, 26.1.0, 26.1.1, 27.0.0, 27.1.0, 27.1.2, 27.2.0, 27.3.0, 27.3.1, 28.0.0, 28.1.0, 28.2.0, 28.3.0, 28.4.0, 28.5.0, 28.6.0, 28.6.1, 28.7.0, 28.7.1, 28.8.0, 28.8.1, 29.0.0, 29.0.1, 30.0.0, 30.1.0, 30.2.0, 30.2.1, 30.3.0, 30.4.0, 31.0.0, 31.0.1, 32.0.0, 32.1.0, 32.1.1, 32.1.2, 32.1.3, 32.2.0, 32.3.0, 32.3.1, 33.1.0, 33.1.1, 34.0.0, 34.0.1, 34.0.2, 34.0.3, 34.1.0, 34.1.1, 34.2.0, 34.3.0, 34.3.1, 34.3.2, 34.3.3, 34.4.0, 34.4.1, 35.0.0, 35.0.1, 35.0.2, 36.0.1, 36.1.0, 36.1.1, 36.2.0, 36.2.1, 36.2.2, 36.2.3, 36.2.4, 36.2.5, 36.2.6, 36.2.7, 36.3.0, 36.4.0, 36.5.0, 36.6.0, 36.6.1, 36.7.0, 36.7.1, 36.7.2, 36.8.0, 37.0.0, 38.0.0, 38.1.0, 38.2.0, 38.2.1, 38.2.3, 38.2.4, 38.2.5, 38.3.0, 38.4.0, 38.4.1, 38.5.0, 38.5.1, 38.5.2, 38.6.0, 38.6.1, 38.7.0, 39.0.0, 39.0.1, 39.1.0, 39.2.0, 40.0.0, 40.1.0, 40.1.1, 40.2.0, 40.3.0, 40.4.0, 40.4.1, 40.4.2, 40.4.3, 40.5.0, 40.6.0, 40.6.1, 40.6.2, 40.6.3, 40.7.0, 40.7.1, 40.7.2, 40.7.3, 40.8.0, 40.9.0, 41.0.0, 41.0.1, 41.1.0, 41.2.0, 41.3.0, 41.4.0, 41.5.0, 41.5.1, 41.6.0, 42.0.0, 42.0.1, 42.0.2, 43.0.0, 44.0.0, 44.1.0, 44.1.1)
  ERROR: No matching distribution found for setuptools>=49.3.0
  ----------------------------------------
ERROR: Command errored out with exit status 1: /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/bin/python /gpfs/ysm/project/dewan/dc2325/conda_envs/py2/lib/python2.7/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-x8e5wp/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- 'setuptools>=49.3.0' 'wheel>=0.34.2' Check the logs for full command output.

This is the error message. I have tried to update steuptools to newer version but it does not seem to work. Is it possible to install LEAP using python 3. Thank you

The same liability score for cases in WTCCC

Hi Omer,

Thanks for developing such good software. I am currently using WTCCC binary traits to create liability scores for downstream analysis.
I first checked if LEAP runs well on my side by doing test.py. I found the liability scores generated in dataset1.phe.liab matches the 6th column in the fam file there. So I assume that my coding there is correct.
And I applied the LEAP there for RA and T1d in WTCCC data. I used the raw genotype data with about 300k SNPs. I have 2938 controls, and different numbers of cases for different traits. I found the liability scores for cases are all the same and are different among controls, which is suspicious. I am wondering if you have any ideas about why it happens there.

Best,
Boran

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.