pandaspgs.sample_set.SampleSet

An object that stores data of type SampleSet. To understand the significance of each column of the DataFrame. Please visit "SampleSet" in PGS Catalog Documentation for details.

Attributes:
  • raw_data –

    list. Convert from obtained JSON data

  • sample_sets –

    DataFrame. It only exists if the parameter mode of constructor is Fat.

  • samples –

    DataFrame. It only exists if the parameter mode of constructor is Fat.

  • cohorts –

    DataFrame. It only exists if the parameter mode of constructor is Fat.

  • mode –

    Fat or Thin. Specifies the mode of the returned object.

 
from pandaspgs.get_sample_set import get_sample_sets

ch = get_sample_sets(pss_id='PSS000001')
ch
ch.raw_data
ch.mode
ch.sample_sets
ch.samples
ch.cohorts

Subset object s by either identifier or position

all_df = get_sample_sets()
all_df[0].sample_sets
all_df[0:3].sample_sets
all_df['PSS000001'].sample_sets
all_df[('PSS000001','PSS000002','PSS000003')].sample_sets

Objects can be manipulated like sets in the mathematical sense.

one = get_sample_sets(pss_id='PSS000001')
two = get_sample_sets(pss_id='PSS000002')
three = get_sample_sets(pss_id='PSS000003')
one_and_two = one+two
two_and_three = two+three
only_one = one_and_two - two_and_three
only_two = one_and_two & two_and_three
one_and_two_and_three = one_and_two | two_and_three
one_and_three = one_and_two ^ two_and_three

__init__ 

__init__(data: list = [], mode: str = 'Fat')
Parameters:
  • data (list, default: [] ) –

    Raw JSON data.

  • mode (str, default: 'Fat' ) –

    Fat or Thin. Specifies the mode of the object.