NEWS.md

In magnusdv/pedtools: Creating and Working with Pedigrees and Marker Data

pedtools 2.6.0

This is a large release with several new features, including a few (relatively minor) breaking changes.

Breaking changes

• In pedigree plots, long labels are now automatically folded to an approximate width of 12 characters by default. Use the new argument foldLabs to adjust the folding width, or to switch off folding (foldLabs = FALSE).

• When adding children or parents to a pedigree, the default labelling of new individuals has been simplified. The new labels are now always the smallest integers not already in use. (Previous versions used "NN_1", "NN_2", etc for pedigrees with non-numeric labels.)

• labels(x) now always returns a character vector, also when x is a list of pedigrees. Use labels(x, unlist = FALSE) to retain the old behaviour.

New features

• addChildren(x, ...), and its companions addSon() and addDaughter(), now works across components of x, when x is a list of pedigrees. For instance, this now works as expected: singletons(1:2, sex = 1:2) |> addSon(1:2).

• New function addChild() is similar to addSon() and addDaughter(), but allows the sex to be set programmatically, also to sex = 0.

• plot.ped() gains argument textAnnot allowing highly customisable text annotations around and inside pedigree symbols.

• ancestors(), descendants(), commonAncestors() and commonDescendants() gain a new argument maxGen limiting the analysis to the given number of generations.

• transferMarkers() gains the argument checkAttrs for checking consistency of marker attributes across pedigree components.

• New function .setSNPfreqs() for modifying allele frequencies when all markers are biallelic. (Experimental; not yet exported.)

Bug fixes

• addSon() and addDaughter() now fail more gracefully if a parent ID is duplicated.

• Fixed regression error in selectMarkers().

pedtools 2.5.0

New features

• New functions maskPed() and unmaskPed() for anonymising pedigree data, and restoring them.

• New function setAlleleLabels() for changing the allele labels of a marker.

• The .pedScaling() gains arguments autoScale and minsize.

• readPed() gains argument colSkip, useful e.g., when reading .ped files with an AFF column.

• The relabel() function for relabelling individuals now allows the argument new to be a function, taking the old labels as input. For instance, relabel(x, toupper) gives upper-case labels for everyone.

Bug fixes

• Preserve the class attribute of MARKERS when subsetting.

pedtools 2.4.0

New features

• The plot() method now handles general (unnested) lists of ped objects. This means that, for instance, with x = list(nuclearPed(1), cousinPed(1), singleton(1)), the command plot(x) simply works. Previously all ped lists had to be handled by plotPedList(). (This is still needed for finer control of each component, and with nested lists.)

• nMarkers() and hasMarkers() have a new argument compwise for more detailed output for ped lists.

• linearPed(0) now produces a singleton (instead of an error).

• setAfreq() now automatically updates the mutation model of the affected marker, if present.

• readFreqDatabase() now accepts frequency files using the long format of MERLIN.

• readFreqDatabase() gains a logical argument scale1, which, if TRUE, scales all vectors to sum 1.

pedtools 2.3.1

New features

• New function singletons() for creating a list of singletons.

• New S3 summary() method handling lists of (possibly disconnected) pedigrees.

• setGenotype() can set the genotype of multiple individuals or markers in the same call. Also, individuals can be specified with selector functions like leaves() and founders(), as in: nuclearPed() |> addMarker() |> setGenotype(ids = founders, geno = "1/2").

• plot.ped() gains argument trimLabs, defaulting to TRUE, which removes line breaks at the start of ID labels. For example: nuclearPed() |> addMarker(geno = c("a/a", "b/b", NA)) |> plot(marker = 1, labs = "1"). (Compare with plot(..., trimLabs = F).)

• The showEmpty argument of plot.ped() is more user friendly, allowing for instance: nuclearPed() |> addMarker() |> plot(marker = 1, showEmpty = "1").

• readFreqDatabase() gains an optional argument df, a data frame of allele frequencies in either "list" or "allelic ladder" format. This is useful in cases where the raw data must be read or modified manually for some reason.

• Add CITATION file.

Bug fixes

• Forgotten argument strict in setAfreq() for pedlists.
• Fix glitch affecting textAbove and textInside.
• Fix title in (still experimental) plot.list().
• Fixed interpretation of marker names in setMarkers(x, alleleMatrix).

pedtools 2.2.0

New features

• The pedprobr function setMutationModel() has been moved to pedtools and renamed to setMutmod(). Unlike its predecessor, this has a new argument update, allowing to update existing models (i.e., leaving unspecified parameters unchanged) instead of creating new models from scratch.

• In swapSex() and setSex(), the ids parameter may now be the name of a selector function operating on the input pedigree. This is convenient when piping; for example, x |> setSex(ids = leaves, sex = 0) sets unknown sex for all leaves of x.

• print.ped() now returns the ped object (not the data frame, as before) invisibly.

• plot.ped() gains new arguments fill, lty, lwd and hatchDensity.

• generations() have been rewritten, with new parameter what.

• addMarker() gains argument locusAttr.

Bug fixes

• Fixed a bug in randomPed(), which caused the function to run out of mating options sometimes.

• The pedigree plot alignment fails in some cases (see https://github.com/mayoverse/kinship2/issues/13). When this happens the plot method reverts to DAG mode and gives a warning.

pedtools 2.1.1

New features

• The plot.ped() method has been internally refactored into 5 functions. Three of these calculate various parameters: .pedAlignment(), .pedScaling() and .pedAnnotation(). The remaining two, drawPed() and .annotatePed() actually draw stuff on the graphics device. As indicated by the dot prefixes, these functions are primarily intended for internal use. Nevertheless, they are documented and exported, to make them available for other packages requiring special plot methods. (For example, the latest version of ibdsim2::haploDraw() use this to compute automatic margins.)

• The function randomPed() has been completely rewritten, ensuring that the output is always a connected pedigree. The new version takes as input the total pedigree size (n) and the number of founders (f).

• removeIndividuals() gains an argument remove, taking as value either "ancestors" or "descendants" (possibly abbreviated. The default value ("descendants") behaves as the previous version. A typical application of remove = "ancestors" is to remove founders, as in linearPed(2) |> removeIndividuals(1, remove = "anc").

• Both relabel() and removeIndividuals() gain an argument returnLabs. If TRUE, the functions return a vector of the pedigree members about to be modified/removed, instead of actually performing any changes.

• Pedigree construction is generally faster, due to various code improvements. Also, ped() gains an argument detectLoops, which if set to FALSE may cut runtime significantly in some cases.

• New function setFounderInbreeding(), which is more flexible (and pipe friendly!) than the previous founderInbreeding<-(). The latter will continue to exist.

• More informative summary() for pedigrees.

pedtools 2.0.0

This version introduces a number of changes in the pedigree plotting. The alignment of individuals is still done with kinship2, but the calculation of scaling, margins and symbol sizes are now done in pedtools. As a result, pedigrees plotted with old code may look slightly different.

Breaking changes

• Pedigree symbols should always have the same height/width (e.g., perfect squares for males). Previously, symbols were squished in many cases, sometimes heavily so.

• Pedigrees now always span the entire plot region, which was often not the case before.

• Plotting of singletons has been completely rewritten, and is now done in plot.ped(). The previous method plot.singleton() has been removed. As a result, singleton plots are much more consistent and appear centred in the plot region.

• Some efforts are done to prevent unneeded duplication of founders, for instance in the case of 3/4-siblings: nuclearPed(2) |> addSon(3) |> addSon(4:5) |> plot()

• The default plot margins have been set to 1.

• plotPedList() is better at guessing relative widths.

• Several minor tweaks in plotPedList() in response to changes in plot.ped().

• The function relabel() now has "asPlot" as default, i.e., using the numerical plot order.

New features

• Pedigrees can now be plotted as directed acyclic graphs (DAGs), by adding arrows = TRUE in plot().

• Plotting pedigrees with selfing is now supported, by automatically switching to DAG mode.

• The argument margins in plot() now accepts a single number, making it more user friendly. The default, margins = 1 corresponds to par(mar = c(1,1,1,1)).

Bug fixes

• Reset graphical parameters after plotPedList()

*

pedtools 1.3.0

New features

• New function avuncularPed() for creating aunt/uncle - nephew/niece pedigrees.

• New function addAllele() for extending the allele set of a marker.

• addSon() and addDaughter() are now more flexible. The previous argument parent has been renamed to parents and accepts one or two parents in any order.

• mergePed() has been overhauled. In particular the new argument by makes it much more user friendly.

• setAfreq() gains argument strict.

Other

• Minor improvements of README and vignette.

• Fixed bug in setGenotype() when setting multiple markers.

• Fixed bug ignoring alleles in distributeMarkers().

pedtools 1.2.0

New features

• pedtools now depends on R 4.1 (or later) because of the pipe operator |>.

• New function setSNPs() for creating and attaching a set of SNP markers with given positions and allele frequencies.

• New function distributeMarkers() for creating and attaching equal markers evenly across a set of chromosomes (by default, the human autosomes).

• New function halfSibTriangle() implementing an interesting breeding pattern.

Bug fixes

• transferMarkers() now ignores members of unknown sex when checking compatibility.

• Fixed bug in addMarker() when input is a list of pedigrees.

• Fixed glitches in setMap().

Other

• Various improvements in code and docs.

• Added many tests.

• Rewrite README example to show piping.

pedtools 1.1.0

The main theme of this version is to make pedtools more adapted to piping, e.g., allowing chains of commands like nuclearPed() |> addSon(1) |> addMarker(alleles = 1:2).

New features

• New functions setAfreq(), setChrom(), setGenotype(), setMarkername(), setPosition() for modifying marker attributes. These are alternatives to the previous in-place modifiers afreq<-() a.s.o..

• 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, ...)).

• 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.

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

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

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

pedtools 1.0.1

New features

• New function generations() for counting generations in pedigrees.

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

• plot.ped() gains a new parameter twins.

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

• Added info and links to pedsuite 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.

• 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).

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 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.

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.

pedtools 0.9.0

• Initial CRAN release.

magnusdv/pedtools documentation built on May 14, 2024, 9:30 p.m.