marker_inplace: Set marker attributes

In pedtools: Creating and Working with Pedigrees and Marker Data

Set marker attributes

Description

These S3 methods perform in-place modifications of marker attributes. They work on single marker objects and markers attached to ped objects (or lists of such). Although these functions will continue to exist, we recommend the newer alternatives setGenotype(), setAfreq(), ... in most cases.

Usage

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, ...) <- 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

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, ...) <- 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, ...) <- 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, ...) <- 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.
value	Replacement value(s).
id	The ID label of a single pedigree member.
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

These functions perform in-place modification of x.

See Also

Alternative setters (not in-place): marker_setattr. Marker attribute getters: marker_getattr.

Examples

x = nuclearPed(1)
x = addMarker(x, alleles = 1:2)

# Set genotypes
genotype(x, marker = 1, id = 1) = "1/2"

# Set marker name
name(x, 1) = "M"

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

# Set position
chrom(x, "M") = 1
posMb(x, "M") = 123.45

# Check result
m = marker(x, `1` = "1/2", name = "M", afreq = c(`1` = 0.1, `2` = 0.9),
           chrom = 1, posMb = 123.45)
stopifnot(identical(x$MARKERS[[1]], m))

pedtools documentation built on Nov. 5, 2023, 5:06 p.m.