hybridPlot: Create an image of hybridisation controls

In ammar257ammar/ArrayAnalysis-Bioconductor: ArrayAnalysis

Create an image of hybridisation controls

Description

This function (from functions_imagesQC.R) creates an image of hybridisation controls based on the qc (simpleaffy Bioconductor package) function, which generally only work for chiptypes with perfect match and mismatch probes, but even not for all of those. As such, when these statistics are not provided as parameters, trys are used in this function to compute them internally. Values for which the try fails are not computed, but the script will continue after giving a warning.

Usage

hybridPlot(
  Data,
  quality = NULL,
  plotColors = NULL,
  WIDTH = 1000,
  HEIGHT = 1414,
  POINTSIZE = 24,
  MAXARRAY = 41
)

Arguments

Data	(Status: required) The raw data object (datatype: AffyBatch)
quality	(Status: optional, Default:NULL) object obtained by calling the qc function (simpleaffy).When not provided, it is computed within the function.(datatype: QCStats)
plotColors	(Status: required, Default:NULL) Vector of colors assigned to each array. (datatype: character)
WIDTH	(Status: optional, Default:1000) png image width (datatype: number)
HEIGHT	(Status: optional, Default:1414) png image height (datatype: number)
POINTSIZE	(Status: optional, Default:24) png image point size (datatype: number)
MAXARRAY	(Status: optional, Default:41) threshold to adapt the image to the number of arrays (datatype: number)

Value

Two images. A PNG image of hybridisation controls, called "RawDataSpike-inPlot"

Examples

# hybridPlot(rawData,quality=quality,plotColors)

ammar257ammar/ArrayAnalysis-Bioconductor documentation built on Jan. 29, 2024, 7:21 a.m.