Contents

PolyGeniusFrame

PolyGeniusFrame class

A tibble subclass holding fetched sample-side ("samples") or model-side ("models") tabular data together with its role metadata. Being a tibble, it passes straight to stats::lm(), stats::glm() or survival::coxph() through their data = argument, and to any associate$*()/evaluate$*() function through data =.

Usage

PolyGeniusFrame(
  fields,
  side = c("samples", "models"),
  groups = list(),
  source = NULL
)

S3 method for class 'PolyGeniusFrame'

x[i, j, drop = FALSE]

print.PolyGeniusFrame(x, ...)

Arguments

Argument	Description
`fields`	Named list of column vectors, or anything tibble::as_tibble() accepts. Becomes the frame's columns.
`side`	One of "samples" (default), "models". Which axis the rows are on.
`groups`	Named list of character vectors, default list(). Maps a role name to the column names in that role. Stored as given; the checks that role names refer to real columns run in roles<-, not here.
`source`	Character scalar, or NULL (default). Source label recorded on the frame; NULL records no source attribute at all.
`x`	A PolyGeniusFrame.
`i`	Row and column indices, as for [ on a tibble.
`j`	Row and column indices, as for [ on a tibble.
`drop`	Logical scalar, default FALSE. Passed to the base subset method; unlike a plain data frame, a one-column result stays a frame unless drop = TRUE is asked for.
`...`	Passed to the underlying tibble printer.

Value

A tibble with S3 class PolyGeniusFrame, carrying the side and groups attributes and, when source was supplied, source.

[ returns a PolyGeniusFrame carrying the original side, source and errors attributes, with each role narrowed to the columns that survived the subset. When the base method returns something that is not a data frame (a bare column under drop = TRUE), that value is returned unchanged.

print() returns x invisibly. It writes a side/dimension header, the tibble itself, and, when the frame carries an errors attribute, the fetch errors below it.

Details

The frame carries three attributes: side, groups (the role mapping, read and written with roles()) and, when a source label was given, source. Roles hold column names, never data vectors. A frame produced by a partly failing fetch also carries an errors attribute, which print() reports below the table.

Where a PolyGeniusFrame comes from

PolyGeniusFrame() is rarely called directly: it is the return type of study$fetch(...), which evaluates unquoted expressions against a PolyGeniusStudy's planes and packs whatever resolves at sample length into a side = "samples" frame and whatever resolves at model length into a side = "models" frame. A fetch touching both sides returns the two frames together in a PolyGeniusFrameSet instead.