diffMethPerChr {methylKit} | R Documentation |
This function gets number of hyper/hypo methylated regions/bases from
methylDiff
object.
It can also plot percentages of differentially methylated bases per chromosome.
diffMethPerChr( x, plot = TRUE, qvalue.cutoff = 0.01, meth.cutoff = 25, exclude = NULL, keep.empty.chrom = FALSE, ... ) ## S4 method for signature 'methylDiff' diffMethPerChr( x, plot = TRUE, qvalue.cutoff = 0.01, meth.cutoff = 25, exclude = NULL, keep.empty.chrom = FALSE, ... ) ## S4 method for signature 'methylDiffDB' diffMethPerChr( x, plot = TRUE, qvalue.cutoff = 0.01, meth.cutoff = 25, exclude = NULL, keep.empty.chrom = FALSE, ... )
x |
a |
plot |
TRUE|FALSE. If TRUE horizontal barplots for proportion of hypo/hyper methylated bases/regions |
qvalue.cutoff |
cutoff for q-value |
meth.cutoff |
cutoff for percent methylation difference |
exclude |
names of chromosomes to be excluded from plot |
keep.empty.chrom |
keep chromosome in list / plot, even if it contains no hyper/hypo sites |
... |
extra graphical parameters to be passed to |
plots a piechart or a barplot for percentage of the target features overlapping with annotation
data(methylKit) # get a list of differentially methylated bases/regions per chromosome and overall diffMethPerChr(methylDiff.obj, plot=FALSE,qvalue.cutoff=0.01, meth.cutoff=25,exclude=NULL)