pedtools (version 2.8.0)

marker_getattr: Get marker attributes

Description

S3 methods retrieving marker attributes. They work on single marker objects and markers attached to ped objects (or lists of such).

Usage

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

Value

The associated marker attributes.

Arguments

x

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

...

Further arguments, not used.

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 x.

See Also

Setting marker attributes: marker_setattr and marker_inplace.

Examples

x = nuclearPed(1)
x = addMarker(x) # add empty marker

# Inspect default attributes
alleles(x, marker = 1)
afreq(x, marker = 1)
name(x, marker = 1)  # NA
chrom(x, marker = 1) # NA