CellMix 1.6

Numeric Computations on ExpressionSet objects

Description

The CellMix defines some generics and methods to apply numeric transformations to ExpressionSet objects, which is convenient when working on gene expression deconvolution algorithms, where scale (log/linear) may matter.

log log-transforms the expression matrix of ExpressionSet objects.

expb applies an entry-wise exponential transformation to the expression matrix of ExpressionSet, in a specific base.

quantile computes the range of expression values in ExpressionSet objects.

Usage

S4 (ExpressionSet)
`log`(x, ...)

expb(x, ...)

S4 (matrix)
`expb`(x, base = exp(1))

S4 (ExpressionSet)
`exp`(x)

S4 (ExpressionSet)
`range`(x, ..., na.rm = FALSE)

S3 (ExpressionSet)
`quantile`(x, ...)

Arguments

x
an ExpressionSet object.
...
extra arguments passed to subsequent calls, usually of the corresponding method in the stats package.
base
log base to use.
na.rm
logical, indicating if NA's should be omitted.

Methods

  1. expsignature(x = "ExpressionSet"): exp is equivalent to expb(x, 1).

  2. rangesignature(x = "ExpressionSet"): range computes the range of expression values from ExpressionSet objects.