plot.gc {cobindR} | R Documentation |
plot.gc calculates the GC (or CpG) content based on a window size for each sequence and plots the content for all sequences as a heatmap over position and sequence.
## S4 method for signature 'cobindr' plot.gc(x, seq.ids, cpg = F, wind.size = 50, sig.test = F, hm.margin = c(4, 10), frac = 10, n.cpu = NA)
x |
an object of the class "cobindr", which will hold all necessary information about the sequences. |
seq.ids |
list of sequence identifiers, for which the GC (or CpG) content will be plotted. |
cpg |
logical flag, if cpg=TRUE the CpG content rather than the GC content will be calculated and plotted. |
wind.size |
integer describing the window size for GC content calculation |
sig.test |
logical flag, if sig.test=TRUE wilcoxon.test is performed per individual window against all windows in other sequence at the same position. The significance test might be slow for large number of sequences |
hm.margin |
optional argument providing the margin widths for the heatmap (if sig.test=FALSE) |
frac |
determines the overlap between consecutive windows as fraction wind.size/frac |
n.cpu |
number of CPUs to be used for parallelization. Default value is 'NA' in which case the number of available CPUs is checked and than used. |
Robert Lehmann <r.lehmann@biologie.hu-berlin.de>
library(Biostrings) n <- 50 # number of input sequences l <- 100 # length of sequences bases <- c("A","C","G","T") # alphabet # generate random input sequences with two groups with differing GC content seqs <- sapply(1:(3*n/4), function(x) paste(sample(bases, l, replace=TRUE, prob=c(.3,.22,.2,.28)), collapse="")) seqs <- append(seqs, sapply(1:(n/4), function(x) paste(sample(bases, l, replace=TRUE, prob=c(.25,.25,.25,.25)), collapse=""))) #save sample sequences in fasta file tmp.file <- tempfile(pattern = "cobindr_sample_seq", tmpdir = tempdir(), fileext = ".fasta") writeXStringSet(DNAStringSet(seqs), tmp.file) cfg <- new('configuration') slot(cfg, 'sequence_type') <- 'fasta' slot(cfg, 'sequence_source') <- tmp.file # avoid complaint of validation mechanism slot(cfg, 'pfm_path') <- system.file('extdata/pfms',package='cobindR') slot(cfg, 'pairs') <- '' runObj <- new('cobindr', cfg, 'test') plot.gc(runObj, cpg = TRUE) unlink(tmp.file)