meltingBatch {rmelting} | R Documentation

## 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")

[Package rmelting version 1.2.0 Index]