hiQuantAdjust: Relate the intensities in each previously medMad-normalized...

In jtheorell/pixSum: Summation of pixel intensities above threshold in png images and tiff movies

Description

This function takes a set of image frames, or a set of tiff-movies, that have previously been normalized with the medMadNormSum function, and uses the highQuants portion of the medMadNormSum output to relate them to each other. This is used both to make the individual movie meaningful, but can also be used to make a set of movies, e.g. where both controls and interesting samples are present, relate to each other, so that the top intensity in all the movies dictates the values in all movies.

Usage

hiQuantAdjust(medMadNormImages, medMadOutput, outDir = ".")

Arguments

medMadNormImages	A vector of TIFF movie file names, e.g. generated with list.files(). The input should have been normalized with the medMadNormSumfunction.
medMadOutput	The output from the medMadNormSum function for the run that generated the medMadNormImages.
outDir	Directory where the normalized tiff movies will be saved. Default is to save a new tiff file in the current directory, with the same name as the old file, but with the extension "adjusted_final".

Value

The adjusted tiff movies, saved to the outDir.

Examples

#Load example data.
data(testMovie)

#Run medMadNormSumRes with the output in the current directory
medMadNormSumRes <- medMadNormSum(testMovie)

#Now run the final function
hiQuantAdjust("Test_normalized.tif", medMadNormSumRes)

jtheorell/pixSum documentation built on April 2, 2020, 5:03 a.m.