R: Marker objects

marker {pedtools}

R Documentation

Marker objects

Description

Creating a marker object associated with a pedigree. The function marker() returns a marker object, while addMarker() first creates the marker and then attaches it to x.

Usage

marker(
  x,
  ...,
  geno = NULL,
  allelematrix = NULL,
  alleles = NULL,
  afreq = NULL,
  chrom = NA,
  posMb = NA,
  name = NA,
  mutmod = NULL,
  rate = NULL,
  NAstrings = c(0, "", NA, "-"),
  validate = TRUE,
  validateMut = validate
)

addMarker(
  x,
  ...,
  geno = NULL,
  allelematrix = NULL,
  alleles = NULL,
  afreq = NULL,
  chrom = NA,
  posMb = NA,
  name = NA,
  mutmod = NULL,
  rate = NULL,
  locusAttr = NULL,
  NAstrings = c(0, "", NA, "-"),
  validate = TRUE
)

Arguments

`x`	A `ped` object.
`...`	One or more expressions of the form `id = genotype`, where `id` is the ID label of a member of `x`, and `genotype` is a numeric or character vector of length 1 or 2 (see Examples).
`geno`	A character vector of length `pedsize(x)`, with genotypes written in the format "a/b".
`allelematrix`	A matrix with 2 columns and `pedsize(x)` rows. If this is non-NULL, then `...` must be empty.
`alleles`	A character containing allele names. If not given, and `afreq` is named, `names(afreq)` is used. The default action is to take the sorted vector of distinct alleles occurring in `allelematrix`, `geno` or `...`.
`afreq`	A numeric of the same length as `alleles`, indicating the population frequency of each allele. A warning is issued if the frequencies don't sum to 1 after rounding to 3 decimals. If the vector is named, and `alleles` is not NULL, an error is raised if `setequal(names(afreq), alleles)` is not TRUE. If `afreq` is not specified, all alleles are given equal frequencies.
`chrom`	A single integer: the chromosome number. Default: NA.
`posMb`	A nonnegative real number: the physical position of the marker, in megabases. Default: NA.
`name`	A character string: the name of the marker. Default: NA.
`mutmod`, `rate`	Mutation model parameters to be passed on to `pedmut::mutationModel()`; see there for details. Note: `mutmod` corresponds to the `model` parameter. Default: NULL (no mutation model).
`NAstrings`	A character vector containing strings to be treated as missing alleles. Default: `c("", "0", NA, "-")`.
`validate`	A logical indicating if the validity of the marker object should be checked. Default: TRUE.
`validateMut`	A logical indicating if the mutation model (if present) should be checked.
`locusAttr`	A list with names `alleles`, `afreq`, `chrom`, `name`, `posMb`, `mutmod`, `rate` (or a subset of these). This can be used as an alternative to entering the arguments as function parameters.

Value

An object of class marker. This is an integer matrix with 2 columns and one row per individual, and the following attributes:

alleles (a character vector with allele labels)
afreq (allele frequencies; default rep.int(1/length(alleles), length(alleles)))
chrom (chromosome number; default = NA)
posMb (physical location in megabases; default = NA)
name (marker identifier; default = NA)
mutmod (a list of two (male and female) mutation matrices; default = NULL)

Examples

x = nuclearPed(father = "fa", mother = "mo", children = "child")

# An empty SNP with alleles "A" and "B"
marker(x, alleles = c("A", "B"))

# Creating and attaching to `x`
addMarker(x, alleles = c("A", "B"))

# Alleles/frequencies can be given jointly or separately
stopifnot(identical(
  marker(x, afreq = c(A = 0.01, B = 0.99)),
  marker(x, alleles = c("A", "B"), afreq = c(0.01, 0.99)),
  ))

# Genotypes can be assigned individually ...
marker(x, fa = "1/1", mo = "1/2")

# ... or using the `geno` vector (all members in order)
marker(x, geno = c("1/1", "1/2", NA))


# Attaching a marker to the pedigree
m = marker(x) # By default a SNP with alleles 1,2
x = setMarkers(x, m)

# A marker with a "proportional" mutation model,
# with different rates for males and females
mutrates = list(female = 0.1, male = 0.2)
marker(x, alleles = 1:2, mutmod = "prop", rate = mutrates)