Poisson Models for Quantifying DNA Copy-number from FISH Images of Tissue Sections

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Documentation for package ‘frenchFISH’ version 1.20.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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areAllNonnegativeIntegers	Helper function to check if all values in the input count matrix are either NA, NaN, or non-negative integers
checkAutomaticCountsEstimatesArguments	Helper function to check the arguments input to getAutomaticCountsEstimates
checkManualCountsEstimatesArguments	Helper function to check the arguments input to getManualCountsEstimates
convertFishalyserCsvToCountMatrix	Function to convert CSV output of the FISHalyseR automatic FISH splot counting software to a count matrix suitable for input to frenchFISH's getAutomaticCountsEstimates
generatePPdat	Helper function to convert spot counts and nuclear area measurements into continuous events for Poisson point estimation
getAutomaticCountsEstimates	FrenchFISH function for generating Poisson point estimates of spot counts from spot counts which have been automatically generated.
getAverageVolumeFrac	Helper function to get the average volume of nucleus sampled given the nucleus radius and section height
getManualCountsEstimates	FrenchFISH function for generating volume adjusted spot counts from spots which have been manually counted (uses a Markov chain Monte Carlo method).
getMaxVolumeFrac	Helper function to get the maximum possible volume of nucleus sampled given the nucleus radius and section height
getMinVolumeFrac	Helper function that returns the minimum possible volume of nucleus sampled given the nucleus radius and section height
getVsegFrac	Helper function that returns the fraction of the nucleus sampled for a specified distance from the midpoint