pandaspgs.score.Score

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

Attributes:
  • raw_data –

    list. Convert from obtained JSON data

  • scores –

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

  • samples_variants –

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

  • samples_variants_cohorts –

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

  • trait_efo –

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

  • samples_training –

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

  • samples_training_cohorts –

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

  • ancestry_distribution –

    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_score import get_scores

ch = get_scores(pgs_id='PGS000001')
ch
ch.raw_data
ch.mode
ch.scores
ch.samples_variants
ch.samples_variants_cohorts
ch.trait_efo
ch.samples_training
ch.samples_training_cohorts
ch.ancestry_distribution

Subset object s by either identifier or position

all_df = get_scores()
all_df[0].scores
all_df[0:3].scores
all_df['PGS000001'].scores
all_df[('PGS000001','PGS000002','PGS000003')].scores

Objects can be manipulated like sets in the mathematical sense.

one = get_scores(pgs_id='PGS000001')
two = get_scores(pgs_id='PGS000002')
three = get_scores(pgs_id='PGS000003')
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.