pedtools: marker_attach – R documentation

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marker_attach

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.

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 just a single list of attributes (not a list of lists), then it is repeated to match the number of markers. In particular, the shortcut locusAttributes = "snp-12" sets all markers to be SNPs with alleles 1 and 2.'

Two alternative format of locusAttributes are allowed: If a data.frame or matrix is given, an attempt is made to interpret it as a frequency database in allelic ladder format. Such an interpretation is also attempted if locusAttributes is a list of named frequency vectors (where the names are the allele labels).

Value

A ped object.

Examples

x = singleton(1)
m1 = marker(x, '1' = 1:2)
m2 = marker(x, '1' = 'a')

x = setMarkers(x, m1)
x = addMarkers(x, m2)
x

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

pedtools

Creating and Working with Pedigrees and Marker Data

v0.9.7

GPL-3

Authors

Magnus Dehli Vigeland [aut, cre] (<https://orcid.org/0000-0002-9134-4962>)

Initial release