writeBackgroundImages: Write Background Images

In blima: Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level

Description

This function writes images with background distribution according to foreground before and after background subtraction.

Usage

writeBackgroundImages(b, spotsToGenerate = NULL, imageType = c("jpg", 
    "png", "eps"), channelForeground = "GrnF", channelBackground = "GrnB", 
    SDMultiple = 3, includePearson = FALSE, outputDir = getwd(), 
    width = 505, height = 505)

Arguments

b	Single beadLevelData object.
spotsToGenerate	NULL for generate images for all spots from b. Otherwise specifies logical vector of the length equals to the number of arrays in b with TRUE for images to generate.
imageType	Type of images produced, either jpg, png or eps
channelForeground	Name of channel of foreground.
channelBackground	Name of channel of background.
SDMultiple	Correct on this level.
includePearson	Include Pearson corelation.
outputDir	Directory where to output images.
width	Width of image (default 505 fits well for 86mm 150dpi illustration in Bioinformatics journal:)
height	Height of image

Author(s)

Vojt<c4><9b>ch Kulvait

Examples

if(require("blimaTestingData") && interactive())
{
    #Write background images before and after correction for background into /tmp directory. This function creates two jpg images for condition D. Output files are /tmp/6898481102_D_CORRECTED.jpg and /tmp/6898481102_D.jpg.
    data(blimatesting)
    p = pData(blimatesting[[2]]@experimentData$phenoData)
    spotsToGenerate = p$Group %in% "D";
    writeBackgroundImages(blimatesting[[2]], imageType="jpg", spotsToGenerate=spotsToGenerate, includePearson=FALSE, outputDir="/tmp", width=505, height=505)
}else
{
    print("To run this example, please install blimaTestingData package from bioconductor by running BiocManager::install('blimaTestingData').");
}

blima documentation built on Nov. 8, 2020, 8:15 p.m.