dechiperMeltDNAtime: Calculate melting temperatures from ranges using a specified...

In peterjuv/FunGenPipe: Tools for building function genomics pipelines

Description

Tm is estimated from a range of temperatures (Trange) by finding a max of ThetaDerivative over that range. Tm is set to NA in case of multiple Tm values.

Usage

dechiperMeltDNAtime(
  myGRanges,
  myBSgenome,
  Trange = seq(50, 100, 1),
  ions = 0.2,
  dropMcols = c("seq", "width", "Trange", "ThetaDerivative", "maxThetaDerivative",
    "TmList")
)

Arguments

myGRanges	GRanges, ranges of sequences with a specified genome
myBSgenome	BSgenome object
Trange	Numeric vector of melting temperatures for calculation of Theta derivatives, forwarded to DECIPHER::MeltDNA; optional, default 50:100
ions	Numeric molar sodium equivalent ionic concentration, forwarded to DECIPHER::MeltDNA; optional, default 0.2
dropMcols	Intermediate columns to drop, default c("seq","width",Trange","ThetaDerivative","maxThetaDerivative","TmList"), NULL to include all

Value

GRanges with melting temperatures added to mcols column "Tm" and optional intermediate columns sequences and widths, (max)ThetaDerivative & list of Tms in case max Tm not unique; message execution time

peterjuv/FunGenPipe documentation built on June 18, 2021, 3:38 a.m.