limix.io.bimbam.read_phenotype¶

limix.io.bimbam.read_phenotype(filepath, verbose=True)[source]¶

Read a BIMBAM phenotype file.

Parameters

filepath (str) – File path.

Returns

pandas.DataFrame – DataFrame representation of the file.
verbose (bool) – True for progress information; False otherwise.

Examples

>>> import limix
>>> from limix import file_example
>>>
>>> with file_example("phenotype.gemma") as filepath:
...     print(limix.io.bimbam.read_phenotype(filepath, verbose=False))
trait         0        1        2
sample
0        1.20000 -0.30000 -1.50000
1            nan  1.50000  0.30000
2        2.70000  1.10000      nan
3       -0.20000 -0.70000  0.80000
4        3.30000  2.40000  2.10000

Notes

BIMBAM phenotype files do not explicitly define sample ids (nor trait ids) but their order of appearance is used to associate samples from different files. Therefore, we denote the first sample found in this file as 0, the second as 1, and so on. We apply the same reasoning for trait naming.