Sort pedigree

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Description

Pedigree sort

Usage

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## S3 method for class 'Pedigree'
sort(x, decreasing=FALSE, na.last=TRUE, ..., by="default")

Arguments

x

pedigree, object to be sorted

decreasing

logical, sort order

na.last

logical, control treatment of NAs; check order

...

arguments passed to order, see details

by

character, sort by "default", "pedigree", "generation", or "dtBirth" information, see details

Details

Sorting of the pedigree can be performed in different ways. Since pedigree can contain date of birth, sorting by this would be the most obvious way and it would be the most detailed sort. However, there might be the case that date of birth is not available for some or all individuals. Therefore, this function by default (when by="default") tries to figure out what would be the best way to perform the sort. If date of birth is available for all individuals then date of birth is used for sorting. If not, generation information is used, but only if it is known for all individuals (it should be more or less easy to figure out the generation for all individuals in the pedigree CHECK). Again if not, sorting is done via information in pedigree i.e. ascendants will precede descendants or vice versa. User can always define it's own preference by argument by. When by="dtBirth" or by="generation" sorting is performed via order and its arguments na.last and decreasing can be used. With by="pedigree" argument decreasing has an effect.

Generation values can have different meaning i.e. values might either increase or decrease from ascendants to descendant with the same meaning. This information is stored in attribute generationOrder (at the time of creating the pedigree object via Pedigree) and used for determining the order of sorting if sorting is by generation. The output of the result might therefore be opposite of what user might expect. If that is the case, use argument decreasing as defined in order. Look also into examples bellow.

Value

Sorted pedigree

Author(s)

Gregor Gorjanc

See Also

Pedigree and order

Examples

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  ped <- generatePedigree(nId=5)
  ped <- ped[sample(1:nrow(ped)), ]
  sort(ped)
  ## sort(ped, by="dtBirth")       ## TODO
  sort(ped, by="generation")
  ## try(sort(ped, by="pedigree")) ## TODO

  ## Sorting with decreasing generation values from ascendants to descendants
  ped1 <- generatePedigree(nId=5, generationOrder="decreasing")
  sort(ped1, by="generation")
  sort(ped1, decreasing=TRUE, by="generation")
  sort(ped1, decreasing=FALSE, by="generation")

  ## Sorting with unknown values
  ped[1, "generation"] <- NA
  sort(ped, na.last=TRUE, by="generation")
  sort(ped, na.last=FALSE, by="generation")
  sort(ped, na.last=NA, by="generation")