locusAttributes: Get or set locus attributes

In magnusdv/pedtools: Creating and Working with Pedigrees and Marker Data

Get or set locus attributes

Description

Retrieve or modify the attributes of attached markers

Usage

getLocusAttributes(
  x,
  markers = NULL,
  checkComps = FALSE,
  attribs = c("alleles", "afreq", "name", "chrom", "posMb", "mutmod")
)

setLocusAttributes(
  x,
  markers = NULL,
  locusAttributes,
  matchNames = NA,
  erase = FALSE
)

Arguments

x	A ped object, or a list of such.
markers	A character vector (with marker names) or a numeric vector (with marker indices). If NULL (default), the behaviour depends on matchNames, see Details.
checkComps	A logical. If TRUE, and x is a list of pedigrees, an error is raised if marker attributes differ between components.
attribs	A subset of the character vector c("alleles", "afreq", "name" ,"chrom" ,"posMb", "mutmod", "rate").
locusAttributes	A list of lists, with attributes for each marker.
matchNames	A logical, only relevant if markers = NULL. If TRUE, then the markers to be modified are identified by the 'name' component of each locusAttributes entry. If FALSE, all markers attached to x are selected in order.
erase	A logical. If TRUE, all previous attributes of the selected markers are erased. If FALSE, attributes not affected by the submitted locusAttributes remain untouched.

Details

The default setting markers = NULL select markers automatically, depending on the matchNames argument. If matchNames = FALSE, all markers are chosen If matchNames = TRUE, markers will be matched against the name entries in locusAttributes (and an error issued if these are missing).

Note that the default value NA of matchNames is changed to TRUE if all entries of locusAttributes have a name component which matches the name a an attached marker.

Possible attributes given in locusAttributes 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))

• name : marker name (NA)

• chrom : chromosome number (NA)

• posMb : physical location in megabases (NA)

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

• rate : mutation model parameter (NULL)

Value

• getLocusAttributes : a list of lists

• setLocusAttributes : a modified version of x.

Examples

x = singleton(1)
x = addMarkers(x, marker(x, name = "m1", alleles = 1:2))
x = addMarkers(x, marker(x, name = "m2", alleles = letters[1:2], chrom = "X"))

# Change frequencies at both loci
y = setLocusAttributes(x, markers = 1:2, loc = list(afreq = c(.1, .9)))
getMarkers(y, 1)

# Set the same mutation model at both loci
z = setLocusAttributes(x, markers = 1:2, loc = list(mutmod = "proportional", rate = .1))
mutmod(z, 1)

# By default, the markers to be modified are identified by name
locs = list(list(name = "m1", alleles = 1:10),
            list(name = "m2", alleles = letters[1:10]))
w = setLocusAttributes(x, loc = locs)
getMarkers(w, 1:2)

# If `erase = TRUE` attributes not explicitly given are erased
w2 = setLocusAttributes(x, loc = locs, erase = TRUE)
chrom(w2, 2) # not "X" anymore

# The getter and setter are inverses
newx = setLocusAttributes(x, loc = getLocusAttributes(x))
stopifnot(identical(x, newx))

magnusdv/pedtools documentation built on April 9, 2024, 7:35 a.m.