spatialImages: Create an image per array, containing one to four spatial...

In ammar257ammar/ArrayAnalysis-Bioconductor: ArrayAnalysis

Create an image per array, containing one to four spatial images

Description

This function (from functions_imagesQC.R) creates an image per array, containing one to four spatial images. For any but the raw images, an object obtained by calling fitPLM (affyPLM Bioconductor package) is used. If this object is not provided, it will be computed internally within this function.

Usage

spatialImages(
  Data,
  Data.pset = NULL,
  Resid = TRUE,
  ResSign = TRUE,
  Raw = TRUE,
  Weight = TRUE,
  WIDTH = 1000,
  HEIGHT = 1414,
  POINTSIZE = 24
)

Arguments

Data	(Status: required) The raw data object (datatype: AffyBatch or ExpressionSet)
Data.pset	(Status: optional, Default:NULL) An object obtained by calling fitPLM (affyPLM), used for each but the raw plot. When not provided, it is computed within the function.(datatype: PLMset)
Resid	(Status: optional, Default:TRUE) Should a residual plot be made? (datatype: logical)
ResSign	(Status: optional, Default:TRUE) Should a residual sign plot be made? (datatype: logical)
Raw	(Status: optional, Default:TRUE) Should a raw plot be made? (datatype: logical)
Weight	(Status: optional, Default:TRUE) Should a weight plot be made? (datatype: logical)
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)

Value

Images containing each of the requested plots, one file per array. Naming is ‘virtual_image’ followed by the (sample)name of the array.

Examples

# There are two default calls by the script:
# 1/ Compute only the images showing the residuals of the PLM (if spatialImage parameter is TRUE):
# spatialImages(rawData, Data.pset=rawData.pset, Resid=TRUE, ResSign=FALSE, Raw=FALSE, Weight=FALSE)
# 2/ Compute the four images for all arrays (if PLMimage parameter is TRUE):
# spatialImages(rawData, Data.pset=rawData.pset)
# where rawData.pset has been constructed by calling:
# rawData.pset <- fitPLM(rawData)

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