Built-in pedigree structures are now labelled according to default plotting order. In particular, this means that pedigrees made by halfSibPed(), cousinPed() and halfCousinPed() are ordered differently than before.
In plot.ped(), the parameter skipEmptyGenotypes is replaced by showEmpty, with default value FALSE.
Function xxxFrequencyDatabase() have been renamed to xxxFreqDatabase()
The marker attribute posCm has been removed, to avoid confusion with the physical position.
marker() now checks for duplicated allele labels.
setMarkers() now checks for duplicated marker names (and allele labels, through marker(); see previous point).
readPed() and friends now automatically recognises allele separator “/” when genotypes are written like “a/b”. Other separators must be indicated with sep as before, e.g., readPed(..., sep = ",").
New function getGenotypes(), which is similar to getAlleles(), but returns a matrix of genotypes written as “a/b”.
More flexible conversion of pedigrees to data frames, with new arguments sep and missing in as.data.frame.ped().
New function setMap(), facilitating setting chromosome and physical position attributes.
marker() has a new argument geno, allowing commands like marker(nuclearPed(1), geno = c("a/a", NA, "a/b")).
print.marker() has been overhauled and gives a more coherent output.
halfSibPed() has a new argument type, either “paternal” (default) or “maternal”.
reorderPed() by default orders by numerical value, if all labels are numeric.
plot.ped() has a new argument hint, which is forwarded to kinship2::plot.pedigree(). This is necessary in some cases where the automatic plotting fails to give a nice pedigree. An example is given in ?plot.ped.
plot.ped() gains argument hatched, which will eventually replace shaded.
Added default values allows executing singleton() and nuclearPed() with no input.
Parts of plotPedList() have been restructured. In particular, the new argument groups makes it easier to control grouping and frames. Previous argument frametitles has been renamed to titles, because it also works without frames.
The plot.ped() argument id.labels is now deprecated in favour of the new labs. This works almost as before, with some exceptions documented here. The labs argument should be thought of as who should be labelled rather than what are the labels. For example, with x = singleton(1), the previous plot(x, id.labels = "2") would rename the singleton to “2”. In contrast, plot(x, labs = "2") will not show any label (since x doesn’t have a member named “2”). In general intersect(labs, labels(x)) determines who gets a label.
Another change is that if labs is a function, it is now applied to the pedigree x, not to labels(x). This makes it very easy to apply standard pedigree functions like females(), nonfounders() and typedMembers(), since they can be referred to simply by name: plot(x, labs = females).
The implementation of doubleCousins() is improved, and some edge cases smoothed out, but the final ordering of individuals may be different in some cases now.
writePed() has been partially rewritten, to make it more similar to readPed(). By default, only the “ped” file is written. New logical arguments “famid” and “header” provide further control of this file.
Writing files in merlin format (indicated by merlin = TRUE) is internally now done in a separate function. This option is rarely needed by end users, but is called by e.g. pedprobr::likelihoodMerlin().
Genotype assignment in marker() is more user-friendly now, allowing inputs like marker(singleton("s"), s = "A/B"). Previously, heterozygous genotypes had to be provided allele-wise, e.g., marker(singleton("s"), s = c("A", "B")). The character “/” must be used as allele separator and will always be interpreted as such.
Given the simplicity of the new syntax I recommend that homozygous genotypes are also written out fully, e.g. s = "B/B" instead of the previous (but still functional) s = "B".
New functions commonAncestors() and commonDescendants() for finding common ancestors/descendants of members in a pedigree.
The functions ancestors() and descendants() have a new logical argument, inclusive, indicating if the person itself should be included.
New function setSex(). This is inverse to getSex() in the sense that setSex(x, sex = getSex(x, named = T)) is identical to x, whether x is a single ped object or a list of such (with unique ID labels).
The old swapSex() is often more convenient in practise, since it automatically deals with spouses. One situation where setSex() is the only option, is when one wants to assign unknown sex (sex = 0) to someone.
New function setMap(), which can be used for assigning chromosome and position attributes to marker objects.
New function readFrequencyDatabase() reads databases. Both list formats and allelic ladders are supported.
Marker attributes “chrom” and “name” are now easier to get/set in ped lists.
The relabel() function now also works for ped lists.
relabel() now works correctly in pedigrees with broken loops
mendelianCheck() didn’t always print as intended
labels() function now also works for ped lists (returning a list of vectors).getSex() was buggy; this has been rewritten and made more efficient.New functions for extracting marker properties: emptyMarkers() and nTyped(). These are generic, with methods for marker, ped and list.
The functions allowsMutations(), isXmarker() and nAlleles() are now generic, with methods for marker, ped and list.
plot.ped() now accepts functional forms of the arguments id.labels, shaded and starred. This simplifies certain plotting tasks, allowing calls like plot(cousinPed(1), shaded = founders, starred = leaves).
mutmod<-() now allows to set the same mutation model for multiple markers in one call.
Many utility functions now operate not only on single pedigrees but also on lists of pedigrees. These include chrom(), name(), selectMarkers(), setMarkers(), typedMembers() and untypedMembers(),
selectMarkers() and friends now accepts boolean marker selection, meaning that the markers argument may be a logical vector (of length equal to the number of attached markers).
readPed() is now more careful regarding marker names. In particular, it should now preserve all names exactly as given, and raise an error if encountering duplicated names.