registerAllImages: Align all images in a directory on a target image and extract...

In amelbek/pamgeneAnalyzeR: Extract data from PamGene PamChip images

Usage

Register (align) all the images in a directory on the chosen target.

Arguments

inDirectory	The directory of the Pamgene images to be aligned.
outDirectory	The output directoy to put the extracted signal and registered image on.
target	The Pamgene image to align on.
nLevels	RNiftyReg parameter.
maxIterations	RNiftyReg parameter.
useBlockPercentage	RNiftyReg parameter.
centers.coords	data frame of coordinates of the target image of centers obtained from the find_centers function.
radius	the number of pixels to take from the center to build the circle (default 5).
parallel.sig.extract	if TRUE the signal extraction process will be parallelized (default FALSE).
pamgene.layout.file	merge the Pamgene STK or PTK layout with the extracred values.
parallel.registration	if TRUE the registration process will be parallelized.
extract.signal	if TRUE the basic statistics values of each peptides, left ans right controls and 8 background points will be extracted. if FALSE only the aligned (registered) image will be returned.

Value

Returns for each image a .txt file with the extracted summary statistics for each peptide, left and right controls and 8 background points.

amelbek/pamgeneAnalyzeR documentation built on May 29, 2019, 8:30 a.m.