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

In CpGassoc: Association Between Methylation and a Phenotype of Interest

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

Arguments

x	Object of class "cpg.perm" or "cpg".
...	Arguments to be passed to methods, such as graphical parameters.

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.

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.

Author(s)

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

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

CpGassoc documentation built on Sept. 11, 2024, 5:17 p.m.