Allele matrix manipulation
Functions for getting and setting the genotypes of multiple individuals/markers simultaneously
getAlleles(x, ids = NULL, markers = NULL) setAlleles(x, ids = NULL, markers = NULL, alleles)
x |
A |
ids |
A vector of ID labels. If NULL (default) all individuals are included. |
markers |
A vector of indices or names of markers attaches to |
alleles |
A character of the same format and dimensions as the output of
|
If the alleles argument of setAlleles() is not a matrix, it is recycled
(if necessary), and converted into a matrix of the correct dimensions. For
example, setting alleles = 0 gives a simple way of removing the genotypes
of some or all individuals (while keeping the markers attached).
getAlleles() returns a character matrix with length(ids) rows and
2 * length(markers) columns. The ID labels of x are used as rownames,
while the columns are named <m1>.1, <m1>.2, ... where <m1> is the
name of the first marker, a.s.o.
setAlleles() returns a ped object identical to x, except for the
modified alleles. In particular, all locus attributes are unchanged.
# Setup: Pedigree with two markers
x = nuclearPed(1)
m1 = marker(x, `2` = "1/2", alleles = 1:2, name = "m1")
m2 = marker(x, `3` = "2/2", alleles = 1:2, name = "m2")
x = setMarkers(x, list(m1, m2))
# Extract allele matrix:
mat1 = getAlleles(x)
mat2 = getAlleles(x, ids = 2:3, markers = "m2")
stopifnot(identical(mat1[2:3, 3:4], mat2))
# Remove all genotypes
y = setAlleles(x, alleles = 0)
y
# Setting a single genotype
z = setAlleles(y, ids = "1", marker = "m2", alleles = 1:2)
# Alternative: In-place modification with `genotype()`
genotype(y, id = "1", marker = "m2") = 1:2
stopifnot(identical(y,z))
### Manipulation of pedlist objects
s = transferMarkers(x, singleton("s"))
peds = list(x, s)
getAlleles(peds)
setAlleles(peds, ids = "s", marker = "m1", alleles = 1:2)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.