Getting the active germline subject
Source:R/RcppExports.R
MutationEngine-cash-get_active_germline.RdThis method returns the active germline subject.
Details
The active germline subject is returned as a
data frame in which the column sample reports the
subject name, the columns pop and super_pop contain the
subject population and super population, respectively, and
the column gender declares the subject gender.
See also
MutationEngine$get_germline_subjects() to get the
available germline subjects; MutationEngine$set_germline_subject()
to set the active germline subject.
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
[█████████████████-----------------------] 40% [00m:01s] Loading RS index
[███████████████████████████████---------] 77% [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 data frame
head(m_engine$get_active_germline(), 5)
#> sample pop super_pop gender
#> 1 NA18941 JPT EAS female