processDivMelt: Main Routine of the Diversity Assay Analysis Tool
In DivMelt: HRM Diversity Assay Analysis Tool

Description Usage Arguments Author(s)

View source: R/processDivMelt.R

processDivMelt uses various passed input, output and analysis parameters for performing an analysis on the data from an HIV Diversity Assay. The data consists of fluorescence measures, the analysis identifies candidate melting temperatures, peak changes in fluorescence and other statistics as they relate to the data. Parameters are listed below (default values are in parenthesis).

processDivMelt(dir,
	singleFile,
	selectList,
	sampleMask,
	theta1=50,
	theta2=30,
	format,
	showStats,
	excludeEarly,
	earlyCutoff,
	excludeLate,
	lateCutoff,
	includeShoulders,
	shoulderCutoff,
	showFlorSmooth,
	showDFlorSmooth,
	useLasso,
	t1Cutoff,
	t2Cutoff,
	t1SlopeWindow,
	t2SlopeWindow,
	scoreFile,
	dataFile,
	modelFile,
	rejectsFile,
	statsFile,
	xrangeOverride,
	xrangemin,
	xrangemax,
	progressFunc)

`dir`	directory containing desired ABT/FLO files (required)
`singleFile`	a single file in that directory (for just one file)
`selectList`	a list of samples to plot (searched for in the file or files above), the default is to do all
`sampleMask`	a full or partial sample name or regular expression used to select individual samples
`theta1`	T1 cutoff angle (50 deg)
`theta2`	T2 cutoff angle as absolute value (30 deg)
`format`	format for output plots namely pdf, png or none (pdf)
`showStats`	flag to enable writing of curve statistics on plots (T)
`excludeEarly`	exclude peaks before main peak (T)
`earlyCutoff`	spacing required for exclusion (3 deg C)
`excludeLate`	exclude peaks after main peak (F)
`lateCutoff`	spacing required for exclusion (3 deg C)
`includeShoulders`	include premature shoulders in rising curve (T)
`shoulderCutoff`	fractional height at which to start inclusion (0.1)
`showFlorSmooth`	flag to enable drawing of smoothing curve for Florescence plot (F)
`showDFlorSmooth`	flag to enable drawing of smoothing curve for dFlorescence plot (T)
`useLasso`	flag to indicate whether to use regression model to filter bad data files (T)
`t1Cutoff`	delta temp that Theta 1 must be exceeded for T1 candidates (1 deg C)
`t2Cutoff`	delta temp that Theta 2 must be exceeded for T2 candidates (1 deg C)
`t1SlopeWindow`	Interval used to approximate slope at T1 (1 deg C)
`t2SlopeWindow`	Interval used to approximate slope at T2 (1 deg C)
`scoreFile`	DivMelt score file to compare against
`dataFile`	output file for DivMelt scores
`modelFile`	Alternate Lasso model file saved as an R object
`rejectsFile`	File to which to write names of Lasso rejected samples ("rejected.csv")
`statsFile`	File to which to write statistics like mean, max, etc. - used to help make a Lasso model training set
`xrangeOverride`	Option to override x-axis range (FALSE)
`xrangemin`	Value to use as override to x-axis min (75)
`xrangemax`	Value to use as override to x-axis min (100)
`progressFunc`	Optional function to call during processing passing it the fraction complete as a real