samplePrepPlot: Create an image of sample preparation controls

In ammar257ammar/ArrayAnalysis-Bioconductor: ArrayAnalysis

Create an image of sample preparation controls

Description

This function (from functions_imagesQC.R) creates an image of sample preparation controls based on the yaqc (yaqcaffy 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

samplePrepPlot(
  Data,
  sprep = NULL,
  lys = NULL,
  plotColors = NULL,
  WIDTH = 1000,
  HEIGHT = 1414,
  POINTSIZE = 24,
  MAXARRAY = 41
)

Arguments

Data	(Status: required) The raw data object (datatype: AffyBatch)
sprep	(Status: optional, Default:NULL) A matrix of 3’probe intensities for dap, thr, lys, and phe, taken from an object of class YAQCStats (yaqc function, yaqcaffy). When not provided, it is computed within the function. (datatype: matrix)
lys	(Status: optional, Default:NULL) Matrix of A, M, P calls for the 3’ probeset of Lys on each array, based on results from the detection.p.val function (simpleaffy) . When not provided, it is computed within the function. (datatype: matrix)
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

A PNG image of sample preparation controls, called "RawDataSamplePrepControl"

Examples

# samplePrepPlot(rawData,sprep,lys,plotColors)

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