cpg.length compares the dimensions of the covariates, the independent phenotype, chip, and the matrix of beta values from
cpg.assoc or cpg.perm. If the number of individuals does not match up. Stops the code.
pointsizefunction simply scales the size of the points for the qq-plot for plot.cpg and plot.cpg.perm
cpgassocsummary is used by cpg.work when the phenotypes contains such small amount of variance such that matrix methods
can not be used. Takes an object of class "aov" or "mlm" and gets the test statistics from these objects while avoiding doing a loop
or the list structures which is typically done if one does summary on one of these objects.
cpg.length(indep, numpatients, covariates, chip.id)pointsizefunction(x)
cpgassocsummary(object)
object indep from cpg.assoc, cpg.work or cpg.perm.
The number of column of the object beta.values in cpg.work or cpg.perm or number of columns of beta.val in cpg.assoc
object covariate from cpg.assoc, cpg.work or cpg.perm.
object chip.id from cpg.assoc, cpg.work or cpg.perm.
the p-values from the object "cpg" or "cpg.perm"
An object of "aov" or "mlm"
cpg.length stops the functions if the dimensions do not add up. Used Internally by CpGassoc
pointsizefunction simply returns a vector of equal length of x to be used in plot for the cex option.
cpgassocsummary returns a matrix of columns two and three of the results value of an "cpg" or "cpg.perm" object. This is for the cpg sites with non-missing data
cpg.perm
cpg.assoc
scatterplot
manhattan
plot.cpg.perm