marker_prop: Marker properties

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

Marker properties

Description

These functions are used to retrieve various properties of marker objects. Each function accepts as input either a single marker object, a ped object, or a list of ped objects.

Usage

emptyMarker(x, ...)

## Default S3 method:
emptyMarker(x, ...)

## S3 method for class 'marker'
emptyMarker(x, ...)

## S3 method for class 'ped'
emptyMarker(x, markers = NULL, ...)

## S3 method for class 'list'
emptyMarker(x, markers = NULL, ...)

nTyped(x, ...)

## Default S3 method:
nTyped(x, ...)

## S3 method for class 'marker'
nTyped(x, ...)

## S3 method for class 'ped'
nTyped(x, markers = NULL, ...)

## S3 method for class 'list'
nTyped(x, markers = NULL, ...)

nAlleles(x, ...)

## Default S3 method:
nAlleles(x, ...)

## S3 method for class 'marker'
nAlleles(x, ...)

## S3 method for class 'ped'
nAlleles(x, markers = NULL, ...)

## S3 method for class 'list'
nAlleles(x, markers = NULL, ...)

isXmarker(x, ...)

## Default S3 method:
isXmarker(x, ...)

## S3 method for class 'marker'
isXmarker(x, ...)

## S3 method for class 'ped'
isXmarker(x, markers = NULL, ...)

## S3 method for class 'list'
isXmarker(x, markers = NULL, ...)

allowsMutations(x, ...)

## Default S3 method:
allowsMutations(x, ...)

## S3 method for class 'marker'
allowsMutations(x, ...)

## S3 method for class 'ped'
allowsMutations(x, markers = NULL, ...)

## S3 method for class 'list'
allowsMutations(x, markers = NULL, ...)

Arguments

x	A single marker object or a ped object (or a list of such)
...	Not used.
markers	A vector of names or indices of markers attached to x. By default all attached markers are selected.

Details

emptyMarker() returns TRUE for markers with no genotypes. If the input is a list of pedigrees, all must be empty for the result to be TRUE.

nTyped() returns the number of typed individuals for each marker. Note that if the input is a list of pedigrees, the function returns the sum over all components.

nAlleles() returns the number of alleles of each marker.

isXmarker() returns TRUE for markers whose chrom attribute is either "X" or 23.

allowsMutations returns TRUE for markers whose mutmod attribute is non-NULL and differs from the identity matrix.

Value

If x is a single marker object, the output is a vector of length 1.

Otherwise, a vector of length nMarkers(x) (default) or length(markers), reporting the property of each marker.

Examples

cmp1 = nuclearPed(1)
cmp2 = singleton(10)
loc = list(alleles = 1:2)
x = setMarkers(list(cmp1, cmp2), locus = rep(list(loc), 3))

#-------- nAlleles() ------------
# All markers have 2 alleles
stopifnot(identical(nAlleles(x), c(2L,2L,2L)))

#-------- emptyMarkers() ------------
# Add genotype for indiv 1 at marker 1
genotype(x[[1]], 1, 1) = "1/2"

# Check that markers 2 and 3 are empty
stopifnot(identical(emptyMarker(x), c(FALSE,TRUE,TRUE)),
          identical(emptyMarker(x[[1]]), c(FALSE,TRUE,TRUE)),
          identical(emptyMarker(x[[2]]), c(TRUE,TRUE,TRUE)),
          identical(emptyMarker(x, markers = c(3,1)), c(TRUE,FALSE)))

#-------- nTyped() ------------
stopifnot(identical(nTyped(x), c(1L,0L,0L)))

# Add genotypes for third marker
genotype(x[[1]], marker = 3, id = 1:3) = "1/1"
genotype(x[[2]], marker = 3, id = 10) = "2/2"

# nTyped() returns total over all components
stopifnot(identical(nTyped(x), c(1L,0L,4L)))

#-------- allowsMutations() ------------
# Marker 2 allows mutations
mutmod(x, 2) = list("prop", rate = 0.1)

stopifnot(identical(allowsMutations(x), c(FALSE,TRUE,FALSE)),
          identical(allowsMutations(x, markers = 2:3), c(TRUE,FALSE)))

#-------- isXmarker() ------------
# Make marker 3 X-linked
chrom(x[[1]], 3) = "X"
chrom(x[[2]], 3) = "X"

stopifnot(identical(isXmarker(x), c(FALSE,FALSE,TRUE)))

magnusdv/pedtools documentation built on April 29, 2024, 10:34 p.m.