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PGSLibraryView

A read-only view of one model in a PGSLibrary

A PGSLibraryView is a non-owning (backbone, position) pointer to one model in a shared PolyGeniusBackbone, handed out by PGSLibrary$models. It never serializes the backbone. Apart from $variants, no accessor reads a variant column, so they are safe to call in a loop over set$models: every value comes from the backbone's registry or the owning set's overlay. $variants materializes a fresh copy of the model's variant table on every call.

Usage

S3 method for class 'PGSLibraryView'

nrow(x)

S3 method for class 'PGSLibraryView'

ncol(x)

S3 method for class 'PGSLibraryView'

dim(x)

S3 method for class 'PGSLibraryView'

length(x)

S3 method for class 'PGSLibraryView'

colnames(x, ...)

S3 method for class 'PGSLibraryView'

dimnames(x)

S3 method for class 'PGSLibraryView'

print(x, ...)

S3 method for class 'PGSLibraryView'

format(x, ...)

S3 method for class 'PGSLibraryView'

.DollarNames(x, pattern = "")

S3 method for class 'PGSLibraryView'

x$name

S3 method for class 'PGSLibraryView'

$(x, name) <- value

S3 method for class 'PGSLibraryView'

x[...]

S3 method for class 'PGSLibraryView'

filter(.data, ...)

S3 method for class 'PGSLibraryView'

select(.data, ...)

S3 method for class 'PGSLibraryView'

mutate(.data, ...)

S3 method for class 'PGSLibraryView'

arrange(.data, ...)

S3 method for class 'PGSLibraryView'

slice(.data, ...)

S3 method for class 'PGSLibraryView'

rename(.data, ...)

S3 method for class 'PGSLibraryView'

transmute(.data, ...)

S3 method for class 'PGSLibraryView'

group_by(.data, ...)

S3 method for class 'PGSLibraryView'

ungroup(.data, ...)

S3 method for class 'PGSLibraryView'

summarise(.data, ...)

Arguments

Argument	Description
`x`	A PGSLibraryView.
`...`	Unused. Present for S3 method compatibility.
`pattern`	Character scalar, default "". Regular expression filtering the completion candidates; "" keeps all of them.
`name`	Character scalar. For $ the field to extract; for $<- the field being assigned, where anything but "name" aborts.
`value`	Character scalar. The model's new name.
`.data`	A PGSLibraryView.

Value

nrow(), ncol() and length() return an integer scalar; dim() an integer vector of length 2 (variants, columns); colnames() a character vector; dimnames() the list list(NULL, colnames(x)); .DollarNames() a character vector of candidates; format() a one-line character scalar; print() x invisibly, called for its console output; $<- x invisibly, called for the rename it records on the owning set. [ never returns -- it aborts. The dplyr verbs never return; they always abort.

Details

$variants materializes the model's variant table off the shared dictionary, in genomic order, as a fresh copy safe to mutate: the five base columns, this model's own and its source's pass-through columns, and a column per attached variant annotation, NA where a source does not cover the variant. $backbone resolves the live PolyGeniusBackbone. Everything else is a registry or overlay read that materializes nothing: $name (the owning set's overlay when there is one, else the backbone's own registry), $build, $n.variants, $generation, $gwas, and any extra field a prior mutate.models() attached. Any other name aborts, a real variant column such as $beta included.

dplyr verbs

Every dplyr verb aborts on a view, naming two remedies: call as.PGS() to get an owned PGS and use its verbs, or use the owning PGSLibrary's grammar (set$filter.variants() and friends). The equivalent PGS verb deep-clones the model it operates on, which on a view would mean copying the whole shared dictionary. Refusing keeps that cost from being paid by accident.

Accessors

nrow(), ncol(), dim(), length(), colnames(), dimnames() -- shape, off the registry. ncol() and length() are both the column count.
print(), format() -- a one-line summary, never the variant table. print() says so and returns when the backbone is not registered in this session; format() has no such guard.
.DollarNames() -- tab-completion over a fixed set of view fields (variants, name, build, n.variants, generation, gwas), never the variant columns, which would cost a materialization to enumerate. Call as.PGS(m) first for full completion.
$ -- $variants materializes the variant table; $backbone resolves the live backbone. Every other allowed name is a registry or overlay read. A variant column such as $beta aborts, so no metadata access turns into a materialization unannounced.
$<- -- accepts name only, and writes it into the owning set's registry by reference, renaming the model there and in every other view of the same row. Every other name aborts, as does a rename on a view with no owning set.
[ -- always aborts. A view is not a table; materialize with as.PGS() first.

See Also

Other pgs-objects: PGS(), PGSLibrary(), PolyGeniusBackbone(), PolyGeniusWeightStore

Aliases: PGSLibraryView, nrow.PGSLibraryView, ncol.PGSLibraryView, dim.PGSLibraryView, length.PGSLibraryView, colnames.PGSLibraryView, dimnames.PGSLibraryView, print.PGSLibraryView, format.PGSLibraryView, .DollarNames.PGSLibraryView, $.PGSLibraryView, $<-.PGSLibraryView, [.PGSLibraryView, filter.PGSLibraryView, select.PGSLibraryView, mutate.PGSLibraryView, arrange.PGSLibraryView, slice.PGSLibraryView, rename.PGSLibraryView, transmute.PGSLibraryView, group_by.PGSLibraryView, ungroup.PGSLibraryView, summarise.PGSLibraryView