generation: Calculate generation value
In GeneticsPed: Pedigree and genetic relationship functions

Description Usage Arguments Details Value Author(s) See Also Examples

generation calculates generation value of individuals in given pedigree. generation<- provides a way to properly add generation information into the pedigree.

1 2	generation(x, start=1, generationOrder=NULL) generation(x, generationOrder=NULL, col=NULL) <- value

`x`	pedigree object
`start`	first generation value
`generationOrder`	character, should be generation values "increasing" or "decreasing" through generations, see details
`col`	character, column name in `x` for generation
`value`	generation values for individuals in the pedigree

Generation value for founders is set to value start, which is by default 1, while other individuals get it according to:

G_s = max(G_{1a} + G_{2a} + ... G_{na}) + 1

where G represents generation value for s - individual, a - ascendant e.g. father and mother, where n=2. N might be higher if there are multiple ascendants i.e. this function can also handle pedigrees with higher order ascendants e.g. grandfather.

generationOrder can be used to define "increasing" or "decreasing" order of generation values. If this argument is NULL, which is default, then this information is taken from the pedigree - see Pedigree for more on this issue.

col provides a way to name or possibly also rename generation column with user specified value, say "generazione" in Italian. When col=NULL, which is default, "generation" is used.

A vector of generation values (integers)

Gregor Gorjanc

Pedigree

  # Nonoverlapping pedigree
  ped <- generatePedigree(nId=5, nGeneration=4, nFather=1, nMother=2)
  ped$generation1 <- generation(ped)
  ped

  # Overlapping Pedigree
  ped <- data.frame(     id=c(1, 2, 3, 4, 5, 6, 7),
                     father=c(0, 0, 2, 2, 2, 4, 4),
                     mother=c(0, 0, 1, 0, 3, 3, 5),
                    dtBirth=c(2, 1, 3, 4, 5, 6, 7))
  ped <- Pedigree(ped, unknown=0, dtBirth="dtBirth")
  generation(ped) <- generation(ped)

  # Overlapping pedigree + one individual (4) comes late in pedigree and
  # has no ascendants
  ped <- data.frame(     id=c(1, 2, 3, 4, 5, 6, 7),
                     father=c(0, 0, 2, 0, 2, 4, 4),
                     mother=c(0, 0, 1, 0, 3, 3, 5),
                    dtBirth=c(2, 1, 3, 2, 5, 6, 7))
  ped <- Pedigree(ped, unknown=0, dtBirth="dtBirth")
  generation(ped)
  generation(ped, generationOrder="decreasing",
             col="generazione") <- generation(ped, generationOrder="decreasing")

Loading required package: MASS

Attaching package: 'GeneticsPed'

The following object is masked from 'package:stats':

    family

   id father mother generation sex generation1
1   1     NA     NA          1   1           1
2   2     NA     NA          1   1           1
3   3     NA     NA          1   2           1
4   4     NA     NA          1   2           1
5   5     NA     NA          1   2           1
6   6      1      4          2   1           2
7   7      1      4          2   2           2
8   8      1      4          2   2           2
9   9      1      4          2   2           2
10 10      1      4          2   1           2
11 11      6      9          3   1           3
12 12      6      9          3   2           3
13 13      6      8          3   2           3
14 14      6      9          3   2           3
15 15      6      8          3   2           3
16 16     11     14          4   1           4
17 17     11     14          4   2           4
18 18     11     13          4   1           4
19 19     11     13          4   2           4
20 20     11     13          4   2           4
1 2 3 4 5 6 7 
1 1 2 1 3 3 4