correlFun: Create an image of the intensity correlation values

In ammar257ammar/ArrayAnalysis-Bioconductor: ArrayAnalysis

Create an image of the intensity correlation values

Description

This function (from functions_imagesQC.R) creates an image of the intensity correlation values of the arrays in the raw or normalized dataset (depending on the object passed). It calls correlationPlot (affyQCReport Bioconductor package).

Usage

correlFun(
  Data,
  clusterOption1 = "pearson",
  clusterOption2 = "ward.D2",
  normMeth = "",
  experimentFactor = NULL,
  legendColors = NULL,
  WIDTH = 1000,
  HEIGHT = 1414,
  POINTSIZE = 24,
  MAXARRAY = 41
)

Arguments

Data	(Status: required) The raw data object (datatype: AffyBatch)
clusterOption1	(Status: optional, Default:"Pearson") String indicating the distance function to be used. Possible values are "pearson", “spearman”, or “euclidean”. (datatype: character)
clusterOption2	(Status: optional, Default:"ward") String indicating the hierarchical clustering function to be used. Possible values are "ward", "single", "complete", "average", "mcquitty", "median" or "centroid". (datatype: character)
normMeth	(Status: required when Data is a normalized data object, Default:"") String indicating the normalization method used (see normalizeData function for more information on the possible values). (datatype: character)
experimentFactor	(Status: required, Default:NULL) The factor of groups. (datatype: factor)
legendColors	(Status: required, Default:NULL) Vector of colors assigned to each experimental group. (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 the intensity correlation values of the arrays, called "DataArrayCorrelationPlot"

Examples

# By default, before the normalization the script will call:
# correlFun(Data=rawData)
# and after normalization:
# correlFun(Data=normData, normMeth=normMeth)

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