statDivMelt: Statistical Output for the Diversity Assay Analysis Tool

Description

statDivMelt uses various passed input, output and analysis parameters to performing a statistical analysis of the data from an HIV Diversity Assay. The data consists of fluorescence measures, the analysis identifies charateristics such as minimum, maximum and average flurescence and dFluoresence. These statistics can be used to generate training data for a linear regression model which can be used in order to reject bad data files in future analysis. Parameters are listed below (default values are in parenthesis).

Usage

statDivMelt(dir,
	singleFile,
	selectList,
	theta1=50,
	theta2=30,
	excludeEarly,
	earlyCutoff,
	excludeLate,
	lateCutoff,
	includeShoulders,
	shoulderCutoff,
	t1Cutoff,
	t2Cutoff,
	t1SlopeWindow,
	t2SlopeWindow,
	statsFile)

Arguments

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

theta1

T1 cutoff angle (50 deg)

theta2

T2 cutoff angle as absolute value (30 deg)

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)

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)

statsFile

File to which to write statistics like mean, max, etc. - used to help make a Lasso model training set