marker_prop {pedtools} | R Documentation |
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 |
... |
Not used. |
markers |
A vector of names or indices of markers attached to |
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)))