pedtools: marker_getset – R documentation

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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 class 'marker'
genotype(x, id, ...)

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

genotype(x, ...) <- value

## S3 replacement method for class 'marker'
genotype(x, id, ...) <- value

## S3 replacement method for class 'ped'
genotype(x, marker, id, ...) <- value

mutmod(x, ...)

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

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

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

mutmod(x, ...) <- value

## S3 replacement method for class 'marker'
mutmod(x, ...) <- value

## S3 replacement method for class 'ped'
mutmod(x, marker = NULL, ...) <- value

## S3 replacement method for class 'list'
mutmod(x, marker = NULL, ...) <- value

alleles(x, ...)

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

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

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

afreq(x, ...)

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

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

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

afreq(x, ...) <- value

## S3 replacement method for class 'marker'
afreq(x, ...) <- value

## S3 replacement method for class 'ped'
afreq(x, marker, ...) <- value

## S3 replacement method for class 'list'
afreq(x, marker, ...) <- value

name(x, ...)

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

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

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

name(x, ...) <- value

## S3 replacement method for class 'marker'
name(x, ...) <- value

## S3 replacement method for class 'ped'
name(x, markers = NULL, ...) <- value

## S3 replacement method for class 'list'
name(x, markers = NULL, ...) <- value

chrom(x, ...)

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

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

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

chrom(x, ...) <- value

## S3 replacement method for class 'marker'
chrom(x, ...) <- value

## S3 replacement method for class 'ped'
chrom(x, markers = NULL, ...) <- value

## S3 replacement method for class 'list'
chrom(x, markers = NULL, ...) <- value

posMb(x, ...)

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

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

posMb(x, ...) <- value

## S3 replacement method for class 'marker'
posMb(x, ...) <- value

## S3 replacement method for class '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

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")

pedtools

Creating and Working with Pedigrees and Marker Data

v0.9.7

GPL-3

Authors

Magnus Dehli Vigeland [aut, cre] (<https://orcid.org/0000-0002-9134-4962>)

Initial release