pandasgwas.set_operation

Set operations for objects of same class

# set operation in EFO Trait
from pandasgwas.get_traits import get_traits
from pandasgwas.set_operation import *
traits1 = get_traits(study_id='GCST000854', efo_id='EFO_0001065')
traits2 = get_traits(study_id='GCST000854', efo_uri='http://www.ebi.ac.uk/efo/EFO_0005133')
#Equivalent to traits3 = traits1 + traits2
traits3 = bind(traits1, traits2)
traits1 = get_traits(study_id='GCST000854', efo_id='EFO_0001065')
traits2 = get_traits(study_id='GCST000854', efo_uri='http://www.ebi.ac.uk/efo/EFO_0005133')
#Equivalent to traits3 = traits1 & traits2
traits3 = intersect(traits1, traits2)
traits1 = get_traits(study_id='GCST000854', efo_id='EFO_0001065')
traits2 = get_traits(study_id='GCST000854', efo_uri='http://www.ebi.ac.uk/efo/EFO_0005133')
#Equivalent to traits3 = traits1 - traits2
traits3 = set_diff(traits1, traits2)
traits1 = get_traits(study_id='GCST000854', efo_id='EFO_0001065')
traits2 = get_traits(study_id='GCST000854', efo_uri='http://www.ebi.ac.uk/efo/EFO_0005133')
#Equivalent to traits3 = traits1 ^ traits2
traits3 = set_xor(traits1, traits2)
traits1 = get_traits(study_id='GCST000854', efo_id='EFO_0001065')
traits2 = get_traits(study_id='GCST000854', efo_uri='http://www.ebi.ac.uk/efo/EFO_0005133')
#Equivalent to traits3 = traits1 | traits2
traits3 = union(traits1, traits2)
traits1 = get_traits(study_id='GCST000854')
traits2 = get_traits(study_id='GCST000854')
#Equivalent to traits1 == traits2
set_equal(traits1, traits2)

bind 

bind(
    a: Union[Association, Variant, Study, Trait],
    b: Union[Association, Variant, Study, Trait],
) -> Union[Association, Variant, Study, Trait]

Binds together GWAS Catalog objects of the same class. Note that bind() preserves duplicates whereas union() does not.

Parameters:
Returns:

intersect 

intersect(
    a: Union[Association, Variant, Study, Trait],
    b: Union[Association, Variant, Study, Trait],
) -> Union[Association, Variant, Study, Trait]

Returns the data common to both A and B, with no repetitions

Parameters:
Returns:

set_diff 

set_diff(
    a: Union[Association, Variant, Study, Trait],
    b: Union[Association, Variant, Study, Trait],
) -> Union[Association, Variant, Study, Trait]

Returns the data in A that is not in B, with no repetitions

Parameters:
Returns:

set_equal 

set_equal(
    a: Union[Association, Variant, Study, Trait],
    b: Union[Association, Variant, Study, Trait],
) -> bool

Check if the raw data of a and b are equal

Parameters:
Returns:
  • bool –

    True or False.

set_xor 

set_xor(
    a: Union[Association, Variant, Study, Trait],
    b: Union[Association, Variant, Study, Trait],
) -> Union[Association, Variant, Study, Trait]

Returns the data of A and B that are not in their intersection (the symmetric difference), with no repetitions

Parameters:
Returns:

union 

union(
    a: Union[Association, Variant, Study, Trait],
    b: Union[Association, Variant, Study, Trait],
) -> Union[Association, Variant, Study, Trait]

Returns the combined data from A and B with no repetitions

Parameters:
Returns: