Description Usage Arguments Details Value Author(s) See Also Examples
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.
1 2 3 4 5 6 7 8 |
x |
Object of class |
... |
Arguments to be passed to methods, such as graphical parameters. |
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.
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 |
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 |
Barfield, R.; Kilaru,V.; Conneely, K.
Maintainer: R. Barfield: <rbarfield01@fas.harvard.edu>
cpg.work
cpg.perm
plot.cpg
scatterplot
cpg.combine
manhattan
plot.cpg.perm
sort.cpg.perm
sort.cpg
cpg.qc
cpg.assoc
1 2 3 4 5 | 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
|
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