IBD.mppData {mppR}

IBD coding for mppData objects

Description

The function first converts genotype data into ABH format. Then it calculates within cross identical by descent (IBD) probabilities.

Usage

IBD.mppData(
  mppData,
  het.miss.par = TRUE,
  subcross.ind = NULL,
  par.per.subcross = NULL,
  type,
  F.gen = NULL,
  BC.gen = NULL,
  type.mating = NULL,
  error.prob = 1e-04,
  map.function = "haldane"
)

Arguments

mppData

An object of class mppData. the mppData must have been processed using: create.mppData, QC.mppData, and IBS.mppData.

het.miss.par

Logical value. if het.miss.par = TRUE, the function will use the offspring segregation to try to infer the allele that was transmitted by the heterozygous or missing parent at a particular locus to make the ABH conversion. Default = TRUE.

subcross.ind

Optional character vector specifying to which sub-cross each genotype belong. Default = NULL.

par.per.subcross

Optional three columns Character matrix specifying : 1) the sub-cross indicators; 2) the parents 1 identifiers of the sub-crosses; 3) the parents 2 identifiers of the sub-crosses. Default = NULL.

type

Character indicator for the type of population analyzed: type = "F" for Fn (F cross n generations); type = "BC" for BCn (backcross n generations); type = "BCsFt" for backcross followed by selfing; type = "DH" for double haploids; and type = "RIL" for recombinant inbred lines. For RIL type specify if the population was obtain using selfing or sibling mating using type.mating. If type = "RIL" or "DH", the function does not assume heterozygous marker scores for these populations and convert them into missing (NA).

F.gen

Numeric integer representing the number of F generations. For example F.gen = 2 for F2. Default = NULL.

BC.gen

Numeric integer representing the number of backcross generations. For example BC.gen = 1 for single backcross. Default = NULL.

type.mating

Character specifying for a RIL population if it was obtained by selfing ("selfing") or by sibling mating ("sib.mat"). Default = NULL.

error.prob

Numeric value for assumed genotyping error rate used in the calculation of the penetrance Pr(observed genotype | true genotype). Default = 0.0001.

map.function

Character expression specifying the type of map function used to infer the IBD probabilities. possibility to choose between "haldane", "kosambi","c-f","morgan". Default = "haldane".

Details

The function first transforms genotype data into within cross ABH format. The function takes the parents of the different cross as reference and assigns the following scores: "A" if the offspring score is equivalent to parent 1; "B" if it is equivalent to parent 2; "H" if it is heterozygous. The function attributes NA for missing when: 1) the offspring score is missing; 2) the two parents have the same score; or 3) when at least one parental score is missing.

If a parent score is heterozygous or missing (het.miss.par = TRUE), the assignment rules are the following. If the two parents are heterozygous or one parent is heterozygous and the other missing, the offspring get NA since the parental origin can not be inferred with certainty. If one parent is heterozygous or missing and the second parent is homozygous, the function looks at offspring segregating pattern to infer which allele was transmitted by the heterozygous parent. If this is possible we consider the heteroxzygous parent as homozygous for the transmitted allele and use this allele score for ABH assignment.

The ABH assignment can be performed using sub-cross structure providing information about sub-cross in arguments subcross.ind and par.per.subcross.

Then the function calculates the IBD probabilities using read.cross() and calc.genoprob() functions from the R/qtl package (Broman et al. 2009).

The type of population must be specified in argument type. Different population types are possible: F-type ('F'), back-cross ('BC'), backcross followed by selfing ('BCsFt'), double haploid ('DH'), and recombinant imbred lines ('RIL'). The number of F and BC generations can be specified using F.gen and BC.gen. The argument type.mating specifies if F and RIL populations were obtained by selfing or by sibling mating.

DH and RIL populations are read as back-cross by R/qtl. For these two population types, heterozygous scores will be treated as missing values.

Value

an increased mppData object containing the the same elements as the mppData object provided as argument and the following new elements:

geno.IBD

A R/qtl cross.object containing the IBD probabilities.

n.zigo

Numeric value Indicating the number of different genotypes: 2 (AA/BB) or 3 (AA/AB/BB)

type

Character expression indicating the type of population.

Author(s)

Vincent Garin

References

Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889-890.

Broman, K. W., & Sen, S. (2009). A Guide to QTL Mapping with R/qtl (Vol. 46). New York: Springer.

See Also

create.mppData, QC.mppData, IBS.mppData

Examples

data(mppData_init)

mppData <- QC.mppData(mppData_init)
mppData <- IBS.mppData(mppData = mppData)

mppData <- IBD.mppData(mppData = mppData, het.miss.par = TRUE, type = 'RIL',
                       type.mating = 'selfing')