convert: Convert annmatrix Objects to and from Other Types

In KKPMW/annmatrix: Annotated Matrix: Matrices with Persistent Row and Column Annotations

Convert annmatrix Objects to and from Other Types

Description

Methods for turning R objects to class annmatrix and vice versa.

Usage

as.annmatrix(x)

## Default S3 method:
as.annmatrix(x)

## S3 method for class 'matrix'
as.annmatrix(x)

## S3 method for class 'annmatrix'
as.matrix(x, ...)

is.annmatrix(x)

Arguments

x	an R object.
...	additional arguments to be passed to or from methods.

Details

as.annmatrix will attempt to convert an object to annmatrix.

as.matrix will turn an annmatrix object into a regular matrix.

is.annmatrix checks if the object is an instance of annmatrix.

Value

is.annmatrix returns TRUE if object is of class 'annmatrix' and FALSE otherwise. as.annmatrix methods return an object of class 'annmatrix'. as.matrix returns a regular matrix.

Author(s)

Karolis Koncevičius

Examples

# construct annmatrix object
x <- matrix(rnorm(20*10), 20, 10)
X <- as.annmatrix(x)

X$group  <- rep(c("case", "control"), each = 5)
X$gender <- sample(c("M", "F"), 10, replace = TRUE)
X@chr    <- sample(c("chr1", "chr2"), 20, replace = TRUE)
X@pos    <- runif(20, 0, 1000000)

is.matrix(x)
is.matrix(X)

is.annmatrix(x)
is.annmatrix(X)

as.matrix(X)

KKPMW/annmatrix documentation built on May 19, 2023, 3:34 a.m.