Other CpGassoc Functions {CpGassoc} | R Documentation |
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)
indep |
object |
numpatients |
The number of column of the object beta.values in |
covariates |
object covariate from |
chip.id |
object |
x |
the p-values from the object |
object |
An object of |
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