GetRelM {sequoia}

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,
  directed = TRUE,
  Return = "Matrix",
  Pairs_suffix = "?"
)

Arguments

Pedigree

dataframe with columns id - dam - sire.

Pairs

dataframe with columns ID1 - ID2 - Rel, e.g. as returned by GetMaybeRel. Combining Pedigree and Pairs works best if the relationships are coded as listed below.

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.

directed

logical, distinguish between e.g. ID1=offspring, ID2=mother ('M') and ID1=mother, ID2=offspring ('O')? Defaults to TRUE; if FALSE both are are scored as 'PO', as are father-offspring pairs, and all grandparent– grand-offspring pairs are scored as 'GPO', and avuncular pairs as 'FNA' and 'HNA'. Not (currently) compatible with patmat. When Return='List', each pair is included twice (as ID1-ID2 & ID2-ID1)

Return

'Matrix', 'Array', or 'List'. 'Matrix' returns an N x N matrix with the closest relationship between each pair. 'Array' returns 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. 'List' returns a list with for each of the R considered relationships a 2-column matrix with the IDs of the pairs having such a relationship. The size of the list (in Mb) is much smaller than for the matrix or array, and this is therefore the only format suitable for pedigrees with many thousands of individuals. If Pairs is specified, the only possible return type is 'Matrix'.

Pairs_suffix

symbol added to the relationship abbreviations derived from Pairs, when both Pedigree and Pairs are provided. Can be an empty string.

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'. Double half-avuncular relationships are indicated as both FA and HA.

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

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 or of the List:

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.

FN

Full nephew/niece

HA

Half avuncular

HN

Half nephew/niece

DFC1

Double full first cousin

FC1

Full first cousin

U

Unrelated (or otherwise related)

See Also

ComparePairs for comparing pairwise relationships between two pedigrees; PlotRelPairs.

Examples

Rel.griffin <- GetRelM(Ped_griffin, directed=FALSE)  # few categories
Rel.griffin <- GetRelM(Ped_griffin, patmat=TRUE, GenBack=2)  # many cat.
table(as.vector(Rel.griffin))
# turning matrix into vector first makes table() much faster
PlotRelPairs(Rel.griffin)