CpGassoc (version 2.70)

cpg.GC: cpg.GC and methods for output of function

Description

cpg.GC accepts an object of class "cpg.perm" or "cpg" and returns information regarding Holm and FDR-significance of the GC (genomic control) adjusted test statistics. For "cpg.perm" will return permutation p-values based on the GC-adjusted values from each permutation.

Usage

cpg.GC(x)
  # S3 method for cpg.gc
print(x,...)
  
  # S3 method for cpg.perm.gc
print(x,...)

Value

cpg.GC returns an object of class "cpg.gc" or "cpg.perm.gc"

gc.results

Matrix consisting of GC-adjusted test statistics for each CpG site. Similar to the results output of cpg.assoc.

gc.info

Data frame with information on the number of Holm and FDR significant sites. Will also have the genomic control inflation estimate. Objects from "cpg.perm" will also have information concerning the permutation p-values.

Arguments

x

Object of class "cpg.perm" or "cpg".

...

Arguments to be passed to methods, such as graphical parameters.

Author

Barfield, R.; Kilaru,V.; Conneely, K.
Maintainer: R. Barfield: <[e-mail]>

Details

cpg.GC will display the number of Holm and FDR-significant sites using the genomic control adjusted p-values test statistics. It will also display the estimated genomic control inflation factor.

See Also

cpg.work cpg.perm plot.cpg scatterplot cpg.combine manhattan plot.cpg.perm sort.cpg.perm sort.cpg cpg.qc cpg.assoc

Examples

data(samplecpg,samplepheno,package="CpGassoc")
results<-cpg.assoc(samplecpg,samplepheno$weight,large.data=FALSE)

cpg.GC(results)
##If the genomic inflation factor is less than one there is no need for adjustment