marker_getattr: Get marker attributes

In pedtools: Creating and Working with Pedigrees and Marker Data

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

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

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, ...)

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, ...)

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, ...)

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, ...)

posMb(x, ...)

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

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

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.

Value

The associated marker attributes.

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

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