plot.gc: function to visualize GC content or CpG content of input...

In cobindR: Finding Co-occuring motifs of transcription factor binding sites

Description

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.

Usage

## 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)

Arguments

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.

Author(s)

Robert Lehmann <[e-mail]>

See Also

testCpG

Examples

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)

cobindR documentation built on April 28, 2020, 6:40 p.m.