pedtools (version 1.1.0)

marker_prop: 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, ...)
# S3 method for default
emptyMarker(x, ...)
# S3 method for marker
emptyMarker(x, ...)
# S3 method for ped
emptyMarker(x, markers = seq_len(nMarkers(x)), ...)
# S3 method for list
emptyMarker(x, markers = seq_len(nMarkers(x)), ...)
nTyped(x, ...)
# S3 method for default
nTyped(x, ...)
# S3 method for marker
nTyped(x, ...)
# S3 method for ped
nTyped(x, markers = seq_len(nMarkers(x)), ...)
# S3 method for list
nTyped(x, markers = seq_len(nMarkers(x)), ...)
nAlleles(x, ...)
# S3 method for default
nAlleles(x, ...)
# S3 method for marker
nAlleles(x, ...)
# S3 method for ped
nAlleles(x, markers = seq_len(nMarkers(x)), ...)
# S3 method for list
nAlleles(x, markers = seq_len(nMarkers(x)), ...)
isXmarker(x, ...)
# S3 method for default
isXmarker(x, ...)
# S3 method for marker
isXmarker(x, ...)
# S3 method for ped
isXmarker(x, markers = seq_len(nMarkers(x)), ...)
# S3 method for list
isXmarker(x, markers = seq_len(nMarkers(x)), ...)
allowsMutations(x, ...)
# S3 method for default
allowsMutations(x, ...)
# S3 method for marker
allowsMutations(x, ...)
# S3 method for ped
allowsMutations(x, markers = seq_len(nMarkers(x)), ...)
# S3 method for list
allowsMutations(x, markers = seq_len(nMarkers(x)), ...)

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, in the case that x is a ped object or a list of such. By default all attached markers are selected.

Value

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

If x is a ped object, or a list of such, the output is a vector of the same length as markers (which includes all attached markers by default), reporting the property of each marker.

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.

Examples

# NOT RUN {
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)))

# }