paramlink: as.matrix.linkdat – R documentation

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as.matrix.linkdat

linkdat to matrix conversion

Description

Converts a linkdat object to a matrix (basically following a pre-makeped LINKAGE format), with marker annotations and other info attached as attributes.

Usage

## S3 method for class 'linkdat'
as.matrix(x, include.attrs = TRUE, ...)

restore_linkdat(x, attrs = NULL, checkped = TRUE)

Arguments

`x`	a `linkdat` object. In `restore_linkdat`: A numerical matrix in LINKAGE format.
`include.attrs`	a logical indicating if marker annotations and other info should be attached as attributes. See value.
`...`	not used.
`attrs`	a list containing marker annotations and other `linkdat` info compatible with `x`, in the format produced by `as.matrix`. If NULL, the attributes of `x` itself are used.
`checkped`	a logical, forwarded to `linkdat`. If FALSE, no checks for pedigree errors are performed.

Details

restore_linkdat is the reverse of as.matrix.

The way linkdat objects are created in paramlink, marker data are stored as a list of marker objects. Each of these is essentially a matrix with various attributes like allele frequencies, map info a.s.o.. This format works well for marker-by-marker operations (e.g. likelihoods and LOD scores), but makes it somewhat awkward to operate 'horizontally', i.e. individual-by-individual, for instance if one wants to delete all genotypes of a certain individual, or rearrange the pedigree in some way.

It is therefore recommended to convert the linkdat object to a matrix first, do the necessary manipulations on the matrix, and finally use restore_linkdat. Attributes are often deleted during matrix manipulation, so it may be necessary to store them in a variable and feed them manually to restore_linkdat using the attrs argument.

With default parameters, restore_linkdat(as.matrix(x)) should reproduce x exactly.

Value

For as.matrix: A matrix with x$nInd rows and 6 + 2*x$nMark columns. The 6 first columns describe the pedigree in LINKAGE format, and the remaining columns contain marker alleles, using the internal (numerical) allele coding and 0 for missing alleles. If include.attrs = TRUE the matrix has the following attributes:

markerattr (a list of marker annotations)
available (the availability vector)
model (the disease model, if present)
plot.labels (plot labels, if present)
orig.ids (original individual IDs)

For restore_linkdat: A linkdat object.

Author(s)

Magnus Dehli Vigeland

Examples

x = linkdat(toyped, model=1)
y = restore_linkdat(as.matrix(x))
stopifnot(all.equal(x,y))

# If attributes are lost during matrix manipulation: Use the 'attrs' argument.
xmatr = as.matrix(x)
newmatr = xmatr[-4, ] # NB: attributes are lost here
z = restore_linkdat(newmatr, attrs = attributes(xmatr))

# Should be the same as:
z2 = removeIndividuals(x, 4)
stopifnot(all.equal(z, z2))

paramlink

Parametric Linkage and Other Pedigree Analysis in R

v1.1-2

GPL (>= 2)

Authors

Magnus Dehli Vigeland [aut, cre], Thore Egeland [ctb], Guro Doerum [ctb]

Initial release

2018-01-05