calcTm {HELP} | R Documentation |
Calculate melting temperature (Tm) using the nearest-neighbor base-stacking algorithm and the unified thermodynamic parameters.
calcTm(x, ...)
x |
characters containing nucleotide sequences (ex: "ATCGGAA") or an object of class ExpressionSet |
... |
Additional arguments passed to methods:
\item{strand1.concentration} { numeric value specifying concentration of strand 1 (default is 2e-07)}
\item{strand2.concentration} { numeric value specifying concentration of strand 2 (default is 2e-07)}
\item{method} { character value specifying the Tm algorithm to use (default is "nearest-neighbor"); currently not supported }
|
Returns a numerical value indicating the predicted melting temperature (Tm) of the sequence in degrees Celsius. A value of NA is returned if the function encounters an error that prevents proper Tm calculation.
Reid F. Thompson (rthompso@aecom.yu.edu)
Allawi, H.T. and SantaLucia, J., Jr. (1997) Thermodynamics and NMR of internal G.T mismatches in DNA, Biochemistry, 36, 10581-10594.
calcTm-methods
, base.stacking.thermodynamics
, calcGC
#demo(pipeline,package="HELP") calcTm("GTGTGGCTACAGGTGGGCCGTGGCGCACCTAAGTGAGGACAGAGAACAAC") calcTm("GTGTGGCTACAGGTGGGCCGTGGCGCACCTAAGTGAGGACAGAGAACAAC",strand1.concentration=1E-5,strand2.concentration=2E-8)