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PMBio / limix-backup

http://pmbio.github.io/limix/
Apache License 2.0
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Data into HDF5 format #1

Closed inti closed 10 years ago

inti commented 10 years ago

Hi, I am looking for some help to get genotype/phenotype data into the HDF5 format required by LIMIX. do you have some example scripts or can you point me to the relevant parts of the code?

thanks in advance, Inti

clippert commented 10 years ago

Hi Inti,

We are right now working on better documenting the format. Also we should have a converter from binary plink to hdf5 up within a couple of days.

Christoph

From: Inti Pedroso [mailto:notifications@github.com] Sent: Friday, May 23, 2014 3:13 AM To: PMBio/limix Subject: [limix] Data into HDF5 format (#1)

Hi, I am looking for some help to get genotype/phenotype data into the HDF5 format required by LIMIX. do you have some example scripts or can you point me to the relevant parts of the code?

thanks in advance, Inti

— Reply to this email directly or view it on GitHubhttps://github.com/PMBio/limix/issues/1.

inti commented 10 years ago

Thank you. look forward to it. Inti

On 23/05/14 15:18, clippert wrote:

Hi Inti,

We are right now working on better documenting the format. Also we should have a converter from binary plink to hdf5 up within a couple of days.

Christoph

From: Inti Pedroso [mailto:notifications@github.com] Sent: Friday, May 23, 2014 3:13 AM To: PMBio/limix Subject: [limix] Data into HDF5 format (#1)

Hi, I am looking for some help to get genotype/phenotype data into the HDF5 format required by LIMIX. do you have some example scripts or can you point me to the relevant parts of the code?

thanks in advance, Inti

— Reply to this email directly or view it on GitHubhttps://github.com/PMBio/limix/issues/1.

— Reply to this email directly or view it on GitHub https://github.com/PMBio/limix/issues/1#issuecomment-44014224.

ostegle commented 10 years ago

Hi Inti,

there is now a limix_converter.py in src/interfaces/python/bin. It will be installed if you use scons install and currently supports to conversion from plink (genotype) and a simple csv file (phenotype).

The functionality will be more extensive soon.

Oliver

inti commented 10 years ago

Hi, Thanks, I'll check it. BW, Inti

On 1 June 2014 16:06, ostegle notifications@github.com wrote:

Hi Inti,

there is now a limix_converter.py in src/interfaces/python/bin. It will be installed if you use scons install and currently supports to conversion from plink (genotype) and a simple csv file (phenotype).

The functionality will be more extensive soon.

Oliver

— Reply to this email directly or view it on GitHub https://github.com/PMBio/limix/issues/1#issuecomment-44779896.