meltingBatch: Compute melting temperature of multiple nucleic acid duplexes...

In aravind-j/rmelting: R Interface to MELTING 5

Compute melting temperature of multiple nucleic acid duplexes in batch

Description

Compute the enthalpy and entropy of helix-coil transition, and then the melting temperature of multiple nucleic acid duplexes in batch.

Usage

meltingBatch(
  sequence,
  comp.sequence = NULL,
  environment.out = TRUE,
  options.out = TRUE,
  message.out = TRUE,
  ...
)

Arguments

sequence	A character vector of 5' to 3' sequences of one strand of the nucleic acid duplex (Note: Uridine and thymidine are not considered as identical).
comp.sequence	A character vector of 3' to 5' complementary sequences of the nucleic acid duplex. Complementary sequences are computed by default, but need to be specified in case of mismatches, inosine(s) or hydroxyadenine(s) between the two strands.
environment.out	logical. If TRUE, gives the melting temperature computation environment details in the output. Default is TRUE.
options.out	logical. If TRUE, gives the details about the options (default or user specified) used for melting temperature computation in the output. Default is TRUE.
message.out	logical. If TRUE, gives the error and/or warning messages, if any in the output. Default is TRUE.
...	Arguments for melting temperature computation (See melting).

Value

A data frame of the melting temperature computation results along with the details of environment, options and messages if specified by the arguments environment.out, options.out and message.out respectively.

See Also

melting

Examples

sequence <- c("CAAAAAG", "CAAAAAAG", "TTTTATAATAAA", "CCATCGCTACC",
              "CAAACAAAG", "CCATTGCTACC", "CAAAAAAAG", "GTGAAC", "AAAAAAAA",
              "CAACTTGATATTATTA", "CAAATAAAG", "GCGAGC", "GGGACC",
              "CAAAGAAAG", "CTGACAAGTGTC", "GCGAAAAGCG")

meltingBatch(sequence, nucleic.acid.conc = 0.0004,
             hybridisation.type = "dnadna", Na.conc = 1)

seq <- c("GCAUACG", "CAGUAGGUC", "CGCUCGC", "GAGUGGAG", "GACAGGCUG",
         "CAGUACGUC", "GACAUCCUG", "GACCACCUG", "CAGAAUGUC", "GCGUCGC",
         "CGUCCGG", "GACUCUCUG", "CAGCUGGUC", "GACUAGCUG", "CUCUGCUC",
         "GCGUCCG", "GUCCGCG", "CGAUCAC", "GACUACCUG", "GACGAUCUG")

comp.seq <- c("CGUUUGC", "GUCGGCCAG", "GCGUGCG", "CUCUUCUC", "CUGUGCGAC",
              "GUCGGGCAG", "CUGUUGGAC", "CUGGGGGAC", "GUCUGGCAG", "CGCUGCG",
              "GCUGGCC", "CUGAUAGAC", "GUCGUUCAG", "CUGAGCGAC", "GAGUUGAG",
              "CGCUGGC", "CUGGCGC", "GCUUGUG", "CUGAGGGAC", "CUGCCAGAC")

meltingBatch(sequence = seq, comp.seq = comp.seq, nucleic.acid.conc = 0.0004,
             hybridisation.type = "rnarna", Na.conc = 1,
             method.singleMM = "tur06")

aravind-j/rmelting documentation built on May 16, 2023, 10:47 p.m.