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Getting the germline subjects

Source: R/RcppExports.R
MutationEngine-cash-get_germline_subjects.Rd

This method returns the available germline subjects.

Value

A dataframe the avaiable germline subjects.

Details

The germline subjects method returns a dataframe containing the avaiable germline subjects. The column sample reports the subject name; the columns pop and super_pop contain the subject population and super population, respectively; the column gender declares the subject gender.

See also

MutationEngine$get_active_germline() to get the available germline subjects; MutationEngine$set_germline_subject() to set the active germline.

Examples

# build a mutation engine
m_engine <- MutationEngine(setup_code = "demo")
#> 
 [█---------------------------------------] 0% [00m:00s] Loading context index                             

 [████████████████████████████████████████] 100% [00m:00s] Context index loaded                            

#> 
 [█---------------------------------------] 0% [00m:00s] Loading RS index                                  

 [████████████████------------------------] 38% [00m:01s] Loading RS index                                 

 [███████████████████████████████---------] 75% [00m:02s] Loading RS index                                 

 [████████████████████████████████████████] 100% [00m:02s] RS index loaded                                 

#> 
 [█---------------------------------------] 0% [00m:00s] Loading germline                                  

 [████████████████████████████████████████] 100% [00m:00s] Germline loaded                                 


# get the active germline subject dataframe
head(m_engine$get_germline_subjects(), 5)
#>    sample pop super_pop gender
#> 1 NA18941 JPT       EAS female
#> 2 NA20513 TSI       EUR   male