Access plate effects stored in a cellHTS object.

Description

This generic function accesses plate effects stored in slot rowcol.effects and overall.effects of a cellHTS instance.

Usage

1
plateEffects(object)

Arguments

object

Object derived from class cellHTS that has been normalized by a spatial normalization method. See details.

Value

plateEffects returns a list with two elements: rowcol and overall.

plateEffects[["rowcol"]] corresponds to the contents of slot rowcol.effects of object. This is a 3D array with the same dimensions as Data(object): nr of Features x nr of Samples x nr of Channels of the current cellHTS object.

plateEffects[["overall"]] contains the data stored in slot overall.effects of object. This is a 3D array with dimensions nr Plates x nr Samples x nr Channels of object. Slot overall.effects is only estimated when B score method is used to normalize the data.

Note that these 2 slots accessed by this function were stored after preprocessing the data either using Bscore method or local regression fit (see normalizePlates for details), by setting the option save.model=TRUE.

Author(s)

Ligia Bras ligia@ebi.ac.uk

See Also

cellHTS normalizePlates Bscore spatialNormalization

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