pedtools 1.1.0

The main theme of this version is to make pedtools more pipe friendly, motivated by the recent inclusion of a native pipe |> in base R. While the use of piping is (and will remain) completely optional, it is a fact that many common pedtools tasks lend themselves very naturally to the pipe syntax. To give a quick example, the following chain builds a pedigree and attaches a SNP marker:

x = nuclearPed(nch = 3) |> 
  addSon(parent = "5") |> 
  addMarker("7" = "b/b", alleles = c("a", "b"))

New features

• New functions setAfreq(), setChrom(), setGenotype(), setMarkername(), setPosition() for modifying marker attributes. These are alternatives to the existing in-place modifiers afreq, chrom, ... .

• New function addMarker() which simplifies that common task of creating and attaching a single marker. The command addMarker(x, ...) is equivalent to addMarkers(x, marker(x, ...)). Importantly, the new function facilitates piping, e.g., nuclearPed() |> addMarker().

• The new addMarker() accepts ped lists, so that one can write e.g. list(singleton(1), singleton(2)) |> addMarker("1" = "a/b", alleles = c("a", "b")).

• readPed() gains the argument colSep, which fixes the previous inability to handle names with spaces.

• relabel(x, new = "generations") now gives automatic, generation-aware labelling: I-1, I-2, II-1, ...

• generations() gains argument maxOnly, set to TRUE by default. If FALSE, the function returns the generation number of each individual.

• New function descentPaths(), mostly intended for use in other ped suite packages.

pedtools 1.0.1

New features

• New function generations() for counting generations in a pedigree.

• New function newMarker() (mostly for internal use).

• plot.ped() gains a new parameter twins for plotting MZ and DZ twins.

• father() and mother() now accepts ped lists as input.

• Added info and links to ped suite in README.

Bug fixes

• Fixed bug in getGenotypes() affecting pedigrees with numerical labels.

• Fixed bug in doubleCousins().

pedtools 0.9.7

Breaking changes

• The rarely-used function cousins() (not to be confused with cousinPed()) is temporarily retracted, since it did not work as intended.

New features

• New constructor newPed() (mainly for internal use).

• New function foundersFirst(), moved from the ribd package.

• In addChildren(), unspecified nch is now allowed, and defaults to length(ids) or length(sex).

• transferMarkers() has a new argument checkSex(), and has been made more efficient by skipping redundant validation steps.

• The functions swapSex(), alleles() and internalID() now work for lists of pedigrees.

• getComponent() gained a new argument errorIfUnknown().

Bug fixes

• unrelated() and siblings() have been improved and cleaned of bugs.

• Fixed an obscure bug in plot.singleton().

pedtools 0.9.6

Breaking changes

• getMap(na.action = 1) is re-implemented and now behaves slightly differently. (This was necessary to improve the handling of linked markers in pedprobr::merlin().)

• The order of individuals in linearPed() now always follows the "asPlot" pattern, as for the other basic pedigrees. (Missed this in the previous version.)

New features

• plot.ped() gains arguments textInside, textAbove and carrier.

• transferMarkers() has new arguments fromIds and toIds enabling transfer between differently-named individuals.

• In setMarkers() and friends, the shortcut locusAttributes = "snp-12" may be used to indicate that all supplied markers are SNPs with alleles 1 and 2. Further shortcuts are "snp-ab" and "snp-AB".

• setMap() is extended to ped lists.

pedtools 0.9.5

Breaking changes

• 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.

• Functions 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).

New features

• 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.

pedtools 0.9.4

Breaking changes

• 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().

New features

• 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.

pedtools 0.9.3

New features

• New function readFrequencyDatabase() reads databases. Both list format 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.

Bug fixes

• relabel() now works correctly in pedigrees with broken loops.

• mendelianCheck() didn't always print as intended.

pedtools 0.9.2

New features

• The labels() function now also works for ped lists (returning a list of vectors).

Bug fixes

• The previous version of getSex() was buggy; this has been rewritten and made more efficient.

pedtools 0.9.1

New features

• 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).

Bug fixes

• 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.