sequoia (version 2.3.5)

GetRelM: Matrix with Pairwise Relationships

Description

Generate a matrix or 3D array with all pairwise relationships from a pedigree or dataframe with pairs.

Usage

GetRelM(
  Pedigree = NULL,
  Pairs = NULL,
  GenBack = 1,
  patmat = FALSE,
  Return = "Matrix"
)

Arguments

Pedigree

dataframe with columns id - dam - sire.

Pairs

dataframe with columns ID1 - ID2 - Rel.

GenBack

number of generations back to consider; 1 returns parent-offspring and sibling relationships, 2 also returns grand-parental, avuncular and first cousins.

patmat

logical, distinguish between paternal versus maternal relative pairs? For avuncular pairs, the distinction is never made.

Return

'Matrix' or 'Array'. The former returns an N x N matrix with the closest relationship between each pair, the latter an N x N x R array with for each of the R considered relationships whether it exists between the pair (1) or not (0). See Details below.

Value

If Return='Matrix', an N x N square matrix, with N equal to the number of rows in Pedigree (after running PedPolish) or the number of unique individuals in Pairs. If Return='Array', an N x N x R array is returned, with R, the number of different relationships, determined by GenBack and patmat.

The following abbreviations are used within the returned Matrix, or as names of the 3rd dimension in the Array:

S

Self

M

Mother

P

Father

MP

Mother or Father (patmat=FALSE)

O

Offspring

FS

Full sibling

MHS

Maternal half-sibling

PHS

Paternal half-sibling

XHS

other half-sibling (hermaphrodites)

HS

half-sibling (patmat=FALSE)

MGM

Maternal grandmother

MGF

Maternal grandfather

PGM

Paternal grandmother

PGF

Paternal grandfather

GP

Grandparent (patmat=FALSE)

GO

Grand-offspring

FA

Full avuncular; maternal or paternal aunt or uncle

HA

Half avuncular

FN

Full nephew/niece

HN

Half nephew/niece

FC1

Full first cousin

DFC1

Double full first cousin

U

Unrelated (or otherwise related)

Details

Double relationships are ignored when Return='Matrix', but not when Return='Array'. For example, when A and B are both mother-offspring and paternal siblings (A mated with her father to produce B), only the mother-offspring relationship will be indicated when Return='Matrix'.

Note that full siblings are the exception to this rule: in the Array they will be indicated as 'FS' only, and not as 'MHS' or 'PHS'. Similarly, full avuncular pairs are not indicated as 'HA'.

When Pairs is provided, GenBack and patmat are ignored, and no check is performed if the abbreviations are compatible with other functions.

See Also

ComparePairs for comparing pairwise relationships between two pedigrees; PlotRelPairs.

Examples

# NOT RUN {
data(Ped_griffin)
Rel.griffin <- GetRelM(Ped_griffin, patmat=TRUE, GenBack=2)
table(c(Rel.griffin))
# turning matrix into vector first makes table() much faster
PlotRelPairs(Rel.griffin)

# }