pedtools (version 2.8.0)

marker_inplace: 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 method for marker
genotype(x, id, ...) <- value
# S3 method for ped
genotype(x, marker, id, ...) <- value
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
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, ...) <- 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, ...) <- 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, ...) <- value
# S3 method for marker
posMb(x, ...) <- value
# S3 method for ped
posMb(x, markers = NULL, ...) <- value

Value

These functions perform in-place modification of x.

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.

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))