Methods for Function induceCMAPCollection in Package gCMAP

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Description

This method defines a CMAPCollection by applying thresholds to an element of an eSet-derived object. For example, applying 'induceCMAPCollection' to a matrix of z-scores stored in an NChannelSet, gene sets can be defined for each of the sample columns stored in the object. (See example section).

Usage

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## S4 method for signature 'eSet'
induceCMAPCollection(eset,element,lower=NULL,higher=NULL,sign.sets=TRUE)
## S4 method for signature 'matrix'
induceCMAPCollection(eset,element,...)

Arguments

eset

An object derived from class eSet, e.g. an NChannelSet

element

A character string corresponding to the assayDataElementName of the 'eset' object to which the thresholds should be applied.

lower

The lower threshold. If not 'NULL', genes with a score smaller than 'lower' will be included in the gene set with sign -1. At least one of 'lower' and 'higher' must be specified.

higher

The 'higher' threshold. If not 'NULL', genes with a score larger than 'higher' will be included in the gene set with sign +1. At least one of 'lower' and 'higher' must be specified.

sign.sets

Logical, indicating whether the 'signed' slot of the generated CMAPCollection should be set to 'TRUE' or 'FALSE'. This parameter should be set to 'FALSE' when the 'element' does not contain information about directionality, e.g. if it is a p-value.

...

Any of the additional arguments detailed above.

See Also

CMAPCollection

Examples

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data(gCMAPData)
assayDataElementNames(gCMAPData)
cmap <- induceCMAPCollection(gCMAPData, element="z", lower=-2, higher=2)
cmap
notes(cmap)

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