mutNuCpos: R function for prediction of nucleosome positioning on a...
In nuCpos: An R package for prediction of nucleosome positions

Description Usage Arguments Value Examples

View source: R/mutNuCpos.R

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.

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)

`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.

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.

# 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).