Simpler interface to retrieve a data.frame of PR metrics from a happy_result object.
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a happy result loaded
subset for either insertions
include all records (ALL), only passing (PASS) or with selective filters applied (SEL)
variant subtype of the form
when run with stratification regions, the subset is
the region ID.
suppress info messages
Subsets: hap.py v0.3.7+ writes subsets
TS_boundary by default, corresponding to truth variants
well contained or at the boundary of confident regions. In some
truthsets, those in
TS_boundary will show worse performance
metrics due to issues with variant representation or a partial
Subtypes: Insertion subtypes are of the form:
where the first letter indicates the variant classification:
D deletion; and
C complex. Hap.py bins the lengths of these records
into ranges by ALT allele length in basepairs:
data.frame of Precision-Recall metrics for the
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# figure out prefix from pkg install location happy_input <- system.file("extdata", "happy_demo.summary.csv", package = "happyR") happy_prefix <- sub(".summary.csv", "", happy_input) # load happy result hapdata <- read_happy(happy_prefix) # long deletion PR curve del_pr <- pr_data(hapdata, var_type = "indel", subtype = "D16_PLUS")
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