statgenIBD (version 1.0.9)

calcIBD: Calculate IBD probabilities

Description

Calculate IBD probabilities for different types of populations.

Usage

calcIBD(
  popType,
  markerFile,
  mapFile,
  evalPos = NULL,
  evalDist = NULL,
  grid = TRUE,
  verbose = FALSE
)

Value

An object of class IBDprob, a list with five elements,

map

a data.frame with chromosome and position of the markers.

markers

a 3-dimensional array of IBD probabilities with genotypes, markers and parents as array dimensions.

parents

the parents.

popType

the population type.

Arguments

popType

A character string indicating the type of population. One of DH, Fx, FxDH, BCx, BCxDH, BC1Sx, BC1SxDH, C3, C3DH, C3Sx, C3SxDH, C4, C4DH, C4Sx, C4SxDH (see Details).

markerFile

A character string indicating the location of the file with genotypic information for the population. The file should be in tab-delimited format with a header containing marker names.

mapFile

A character string indicating the location of the map file for the population. The file should be in tab-delimited format. It should consist of exactly three columns, marker, chromosome and position. There should be no header. The positions in the file should be in centimorgan.

evalPos

A data.frame with evaluation positions to which the calculations should be limited.

evalDist

An optional numerical value indicating the maximum distance for marker positions. Extra markers will be added based on the value of grid.

grid

Should the extra markers that are added to assure the a maximum distince of evalDist be on a grid (TRUE) or in between marker existing marker positions (FALSE).

verbose

Should messages indicating the progress of the process be printed?

Details

IBD probabilities can be calculated for many different types of populations. In the following table all supported populations are listed. Note that the value of x in the population types is variable, with its maximum value depicted in the last column.

Population type	Cross	Description	max. x
DH	biparental	doubled haploid population
Fx	biparental	Fx population (F1, followed by x-1 generations of selfing)	8
FxDH	biparental	Fx, followed by DH generation	8
BCx	biparental	backcross, second parent is recurrent parent	9
BCxDH	biparental	BCx, followed by DH generation	9
BC1Sx	biparental	BC1, followed by x generations of selfing	7
BC1SxDH	biparental	BC1, followed by x generations of selfing and DH	6
C3	three-way	three way cross: (AxB) x C
C3DH	three-way	C3, followed by DH generation
C3Sx	three-way	C3, followed by x generations of selfing	7
C3SxDH	three-way	C3, followed by x generations of selfing and DH generation	6
C4	four-way	four-way cross: (AxB) x (CxD)
C4DH	four-way	C4, followed by DH generation
C4Sx	four-way	C4, followed by x generations of selfing	6
C4SxDH	four-way	C4, followed by x generations of selfing and DH generation	6

Examples

## Compute IBD probabilities for Steptoe Morex.
SxMIBD <- calcIBD(popType = "DH",
                  markerFile = system.file("extdata/SxM", "SxM_geno.txt",
                                        package = "statgenIBD"),
                  mapFile = system.file("extdata/SxM", "SxM_map.txt",
                                        package = "statgenIBD"))

## Check summary.
summary(SxMIBD)

## Compute IBD probabilities for Steptoe Morex.
## Add extra evaluation positions in between exiting marker positions
## to assure evaluation positions are at most 5 cM apart.
SxMIBD_Ext <- calcIBD(popType = "DH",
                      markerFile = system.file("extdata/SxM", "SxM_geno.txt",
                                              package = "statgenIBD"),
                      mapFile = system.file("extdata/SxM", "SxM_map.txt",
                                            package = "statgenIBD"),
                      evalDist = 5)

## Check summary.
summary(SxMIBD_Ext)