mutNuCpos {nuCpos} | R Documentation

## R function for prediction of nucleosome positioning on a mutant sequence

### Description

This function plots the results of nucleosome positioning prediction for wild type and mutant sequences in a specified window. Nucleosomal and linker models built upon the chemical maps are used for the calculation. No file is generated in the current directry.

### Usage

    mutNuCpos(wtseq, site = 1, ins = "", del = 0,
        species = "mm", smoothHBA = FALSE, std = FALSE,
        plot.window = 501, prob.dyad = FALSE,
        show.viterbi = FALSE, occup.window = 200,
        show.occup.window = FALSE, ymax.prob = 1.1,
        ymax.occup = 1.1, ylim.HBA = c(-15, 5),
        annotation = data.frame(name = "", color = "", left = 0,
        right = 0)[0, ], full = FALSE)

### Arguments

`wtseq` | a character or DNAString object. The wild-type sequence to be mutated. The string must not contain letters other than "A", "C", "G" or "T."
`site` | an integer. The site of mutagenesis.
`ins` | a character or DNAString object. The sequence to be inserted at the "site." The string must not contain letters other than "A", "C", "G" or "T." `ins=""` indicates no sequence will be inserted.
`del` | an integer. The length of the deleted region that starts at the "site." `del=0` indicates no sequence will be deleted.
`species` | a character = mm, sc or sp; "mm" for mouse, "sc" for S. cerevisiae and "sp" for S. pombe.
`smoothHBA` | a logical value indicating whether smoothing of histone binding affinity should be applied as in the `predNuPoP` function of the parental package NuPoP.
`std` | a logical value indicating whether standardization should be applied to the histone binding affinity score.
`plot.window` | an integer. The window to be plotted. This must be an odd number.
`prob.dyad` | a logical value indicating whether the probability for the predicted dyads is plotted.
`show.viterbi` | a logical value indicating whether the viterbi path is plotted.
`occup.window` | an integer. The size of the window for the calculation of occupancy difference. occup.window=200 means that the sum of the absolute occupancy difference for the left-side and right-side 100-bp regions flanking the "site" is caluculated.
`show.occup.window` | a logical value indicating whether the window for the occupancy difference calculation is shown in the occupancy plots.
`ymax.prob` | an integer. Specify the upper limit of the y axis of the probability plots.
`ymax.occup` | an integer. Specify the upper limit of the y axis of the occupancy plots.
`ylim.HBA` | an integer vector of two values. Specify the lower and upper limits of the y axis of the histone binding affinity plots.
`annotation` | a data frame. Colored bars can be put under the plots.
`full` | a logical value indicating whether the calculation results will be returned as a data frame object.

### Value

When the `full` argument is set as `TRUE`, the prediction results for the mutant sequence will be returned as a data frame object. The data frame has five columns as that produced by `predNuCpos` when its argument `ActLikePredNuPoP` was set as `FALSE`:

`pos` | position in the input DNA sequence
`pstart` | probability that a nucleosome starts at
`nucoccup` | nucleosome occupancy score
`viterbi` | Viterbi path (1 and 0 for the nucleosome and linker states, repsectively)
`affinity` | histone binding affinity score

When the `full` argument was set as `FALSE`, this function returns a named numeric vector, in which the occupancy difference and HBA scores around the target site are stored.

When `ins=""` and `del=0` are applied, two wild-type sequences are used for the calculation and plotting; this yields no difference in the occupancy or HBA.

### Examples

    # Loading the sequence of TALS, a budding yeast
    # minichromosome.
    TALS <- paste(scan(file = system.file("extdata", "TALS.fasta",
        package="nuCpos"), what = character(), skip = 1), sep = "",
        collapse = "")

    # Loading the telomere repeat sequence (hTELx12)
    TTAGGGx12 <- paste(scan(file = system.file("extdata",
        "TTAGGGx12.fasta", package="nuCpos"), what = character(),
        skip = 1), sep = "", collapse = "")
    mutNuCpos(TALS, site = 1464, ins= TTAGGGx12, species="sc",
        prob.dyad = TRUE, smoothHBA=TRUE, plot.window = 601,
        ylim.HBA = c(-11, 0),
        annotation = data.frame(name = "alpha2",
            color = "purple", left = 1534, right = 1559))

    # Loading the telomere repeat isomeric sequence (SI-Ax12)
    TGTAGGx12 <- paste(scan(file = system.file("extdata",
        "TGTAGGx12.fasta", package="nuCpos"), what = character(),
        skip = 1), sep = "", collapse = "")
    mutNuCpos(TALS, site = 1464, ins= TGTAGGx12, species="sc",
        prob.dyad = TRUE, smoothHBA=TRUE, plot.window = 601,
        ylim.HBA = c(-11, 0),
        annotation = data.frame(name = "alpha2",
        color = "purple", left = 1534, right = 1559))

    # DNA sequences used here are from Ichikawa et al. (2014).

[Package nuCpos version 1.12.0 Index]