pedtools 2.7.0
New features
-
plot.ped()
gains a new argument,spouseOrder
, to specify the display order of spouses. -
readPed()
andas.ped()
now include aaddMissingFounders
argument, supporting pedigree files where (some or all) founders are not explicitly listed (i.e., entries in thefid
ormid
columns that do not appear in theid
column). -
readPed()
andas.ped()
now also feature asexCodes
argument, accommodating pedigree files where sex is indicated by codes other than the standard 0 (unknown), 1 (male), 2 (female). -
reorderPed()
has improved flexibility, allowing the reordering of a subset of the pedigree. -
selfingPed()
now accepts a vector of ID labels as the first argument. (Previously, only the number of selfings could be given.) -
The plotting argument
showEmpty
, controlling the appearance of missing genotypes, now accepts a function, e.g.leaves()
.
Other changes
-
getComponent()
behaves better when the pedigree has only one component. -
ped()
checks for illegalsex
entries earlier than before, thus avoiding certain (rare) problems. -
Brush up on code and documentation.