Usage
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)
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
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