pedtools (version 1.0.1)

marker_getset: Get/set marker attributes

Description

These functions can be used to manipulate a single attribute of one or several markers. Each getter/setter can be used in two ways: Either directly on a marker object, or on a ped object which has markers attached to it.

Usage

genotype(x, ...)
# S3 method for marker
genotype(x, id, ...)
# S3 method for ped
genotype(x, markers = NULL, id, ...)
genotype(x, ...) <- value
# S3 method for marker
genotype(x, id, ...) <- value
# S3 method for ped
genotype(x, marker, id, ...) <- value
mutmod(x, ...)
# S3 method for marker
mutmod(x, ...)
# S3 method for ped
mutmod(x, marker, ...)
# S3 method for list
mutmod(x, marker, ...)
mutmod(x, ...) <- value
# S3 method for marker
mutmod(x, ...) <- value
# S3 method for ped
mutmod(x, marker = NULL, ...) <- value
# S3 method for list
mutmod(x, marker = NULL, ...) <- value
alleles(x, ...)
# S3 method for marker
alleles(x, ...)
# S3 method for ped
alleles(x, marker, ...)
# S3 method for list
alleles(x, marker, ...)
afreq(x, ...)
# S3 method for marker
afreq(x, ...)
# S3 method for ped
afreq(x, marker, ...)
# S3 method for list
afreq(x, marker, ...)
afreq(x, ...) <- value
# S3 method for marker
afreq(x, ...) <- value
# S3 method for ped
afreq(x, marker, ...) <- value
# S3 method for list
afreq(x, marker, ...) <- value
name(x, ...)
# S3 method for marker
name(x, ...)
# S3 method for ped
name(x, markers = NULL, ...)
# S3 method for list
name(x, markers = NULL, ...)
name(x, ...) <- value
# S3 method for marker
name(x, ...) <- value
# S3 method for ped
name(x, markers = NULL, ...) <- value
# S3 method for list
name(x, markers = NULL, ...) <- value
chrom(x, ...)
# S3 method for marker
chrom(x, ...)
# S3 method for ped
chrom(x, markers = NULL, ...)
# S3 method for list
chrom(x, markers = NULL, ...)
chrom(x, ...) <- value
# S3 method for marker
chrom(x, ...) <- value
# S3 method for ped
chrom(x, markers = NULL, ...) <- value
# S3 method for list
chrom(x, markers = NULL, ...) <- value
posMb(x, ...)
# S3 method for marker
posMb(x, ...)
# S3 method for ped
posMb(x, markers = NULL, ...)
posMb(x, ...) <- value
# S3 method for marker
posMb(x, ...) <- value
# S3 method for ped
posMb(x, markers = NULL, ...) <- value

Arguments

x

Either a marker object, a ped object or a list of ped objects.

...

Further arguments, not used in most of these functions.

id

The ID label of a single pedigree member.

value

Replacement value(s).

marker, markers

The index or name of a marker (or a vector indicating several markers) attached to ped. Used if x is a ped object.

Value

The getters return the value of the query. The setters perform in-place modification of the input.

Examples

# NOT RUN {
x = nuclearPed(1)
x = setMarkers(x, locusAttributes = list(name = "M", alleles = 1:2))

# Set genotype
genotype(x, marker = "M", id = 1) = 1:2
genotype(x, marker = "M", id = 3) = 1

# Genotypes are returned as a vector of length 2
genotype(x, marker = "M", id = 1)

# Change allele freqs
afreq(x, "M") = c(`1` = 0.1, `2` = 0.9)

# Check the new frequencies
afreq(x, "M")

# }