pandas_plink.Chunk

class pandas_plink.Chunk(nsamples=1024, nvariants=1024)

Chunk specification.

It is effectively a contiguous submatrix of the dosage matrix.

Parameters

• nsamples (Optional[int]) – Number of samples in a single chunk, thresholded by the total number of samples. Set to None to include all samples. Default to 1024.

• nvariants (Optional[int]) – Number of variants in a single chunk, thresholded by the total number of variants. Set to None to include all variants. Default to 1024.

Note

Small chunks might increase computation time while large chunks might increase IO usage. If you have a small data set, try setting both nsamples and nvariants to None. If the data set is too large but your application will use every sample, try to set nsamples = None and choose a small value for nvariants.

Examples

>>> from pandas_plink import Chunk
>>>
>>> Chunk()
Chunk(nsamples=1024, nvariants=1024)
>>> Chunk(nsamples=None)
Chunk(nsamples=None, nvariants=1024)

__init__(nsamples=1024, nvariants=1024)

Initialize self. See help(type(self)) for accurate signature.