pedigreePairwiseRelatedness: Assign relatedness from pedigree data

In smgogarten/GWASTools: Tools for Genome Wide Association Studies

Assign relatedness from pedigree data

Description

This function assigns relationships from pedigree data. Output includes the theoretical pairwise kinship coefficients.

Usage

pedigreePairwiseRelatedness(pedigree)

Arguments

pedigree

A dataframe containing the pedigree information for the samples to be examined with columns labeled "family", "individ", "mother", "father" and "sex" containing the identifiers for family, individual, individual's mother, individual's father and individual's sex (coded as "M" or "F") . Identifiers can be integer, numeric or character but identifiers for mother and father for founders are assumed to be 0. Error messages are returned for pedigree inconsistencies. See pedigreeCheck

Details

Assigns relationships between individuals in a pedigree, including "U" = unrelated, "PO" = parent/offspring, "FS" = full siblings, "HS" = half siblings, "Av" = avuncular, "FC" = first cousins, "GpGc" = grandparent-grandchild, "HAv" = half-avuncular, "HFC" = half-first-cousin, "GGp" = great-grandparent-great-grandchild, "GAv" = grand-avuncular, "HSFC" = half-sib-first-cousin, "DFC" = double first cousin, among others. Relatedness is not calculated for inbred families but kinship coefficients are.

Value

A list with the following components:

inbred.fam	A vector of id's of families with inbreeding (relationships are not assigned).
inbred.KC	A dataframe for inbred families with columns "Individ1","Individ2", "kinship" and "family" containing the id's of the pair of individuals, kinship coefficient and family id.
relativeprs	A dataframe with columns "Individ1", "Individ2", "relation", "kinship" and "family" containing the id's of the pair of individuals, the relationship between the individuals if closely related (possible values are "U" = unrelated, "PO" = parent/offspring, "FS" = full siblings, "HS" = half siblings, "Av" = avuncular, "GpGc" = grandparent-grandchild, and "FC" = first cousins, among others), kinship coefficient and family id.

Author(s)

Cecelia Laurie

See Also

pedigreeCheck, pedigreeMaxUnrelated

Examples

family <- c(1,1,1,1,2,2,2,2,2,2,2)
individ <- c(1,2,3,4,5,6,7,8,9,10,11)
mother <- c(0,0,1,1,0,0,5,5,0,0,10)
father <- c(0,0,2,2,0,0,6,9,0,0,7)
sex <- c("F","M","F","F","F","M","M","M","M","F","F")
pedigree <- data.frame(family, individ, mother, father, sex, stringsAsFactors=FALSE)
pedigreePairwiseRelatedness(pedigree)

# inbred family
family <- rep(2,7)
individ <- paste("I",c(1,2,3,4,5,6,7),sep="")
mother <- c(0,0,0,"I1","I1","I3","I5")
father <- c(0,0,0,"I2","I2","I4","I4")
sex <- c("F","M","F","M","F","F","F")
samp2 <- data.frame(family, individ, mother, father, sex, stringsAsFactors=FALSE)
pedigreePairwiseRelatedness(samp2)

smgogarten/GWASTools documentation built on Nov. 10, 2024, 9:54 p.m.