marker_attach: Attach markers to pedigrees

In pedtools: Creating and Working with Pedigrees and Marker Data

Attach markers to pedigrees

Description

In many applications it is useful to attach markers to their associated ped object. In particular for bigger projects with many markers, this makes it easier to manipulate the dataset as a unit. The function setMarkers() replaces all existing markers with the supplied ones, while addMarkers() appends the supplied markers to any existing ones. Note that there is also the function addMarker(), which creates and attaches a single marker in one go.

Usage

setMarkers(
  x,
  m = NULL,
  alleleMatrix = NULL,
  locusAttributes = NULL,
  missing = 0,
  sep = NULL,
  checkCons = TRUE
)

addMarkers(
  x,
  m = NULL,
  alleleMatrix = NULL,
  locusAttributes = NULL,
  missing = 0,
  sep = NULL,
  checkCons = TRUE
)

Arguments

x	A ped object
m	Either a single marker object or a list of marker objects
alleleMatrix	A matrix with pedsize(x) rows, containing the observed alleles for one or several markers. The matrix must have either 1 or 2 columns per marker. If the former, then a sep string must be a given, and will be used to split all entries.
locusAttributes	A list of lists, with attributes for each marker. See Details for possible attributes.
missing	A single character (or coercible to one) indicating the symbol for missing alleles.
sep	If this is a single string, each entry of alleleMatrix is interpreted as a genotype, and will be split by calling strsplit(..., split = sep, fixed = TRUE). If alleleMatrix contains entries with "/", this will be taken as separator by default. (To override this behaviour, put sep = FALSE.)
checkCons	A logical. If TRUE (default), each marker is checked for consistency with x.

Details

The most general format of locusAttributes a list of lists, one for each marker, where possible entries in the inner lists are as follows (default values in parenthesis):

• alleles : a character vector with allele labels

• afreq : a numeric vector with allele frequencies (rep.int(1/L, L), where L = length(alleles))

• chrom : chromosome number (NA)

• posMb : physical location in megabases (NA)

• name : marker name (NA)

• mutmod : mutation model, or model name (NULL)

• rate : mutation model parameter (NULL)

If locusAttributes is a single list of attributes (not a list of lists), then it is repeated to match the number of markers.

Alternative formats of locusAttributes:

• data frame or matrix. In this case an attempt is made to interpret it as a frequency database in ⁠allelic ladder⁠ format.

• A list of frequency vectors. All vectors should sum to 1, and be named (with allele labels)

• Shortcut for simple SNP data: The argument locusAttributes = "snp-AB" sets all markers to be equifrequent SNPs with alleles A and B. The letters A and B may be replaced by other single-character letters or numbers.

Value

A ped object.

See Also

addMarker()

Examples

x = singleton(1)
m1 = marker(x, `1` = "1/2")
m2 = marker(x, `1` = "a/b")

# Attach to x
x1 = setMarkers(x, list(m1, m2))

# Reversing the order of the markers
setMarkers(x, list(m2, m1))

# Alternative syntax, adding one marker at a time
x2 = x |>
  addMarker(`1` = "1/2") |>
  addMarker(`1` = "a/b")

stopifnot(identical(x1, x2))

pedtools documentation built on Nov. 5, 2023, 5:06 p.m.