Description Usage Arguments Value Note Examples
Returns information about the top cluster in the GEE analysis
1 | summarize.top.clusters(betas, covariates, exposure, id, clusters.GEE.results = NULL, clusters.GEE.results.file = NULL, minimum.sites = 2, top.number = 10, cutoff.fdr.pval = 0.05, cutoff.effect.size = NULL, annot = NULL, annotation.file.name = NULL, required.annotation = c("IlmnID", "Coordinate_36", "UCSC_RefGene_Name", "UCSC_RefGene_Group", "UCSC_CpG_Islands_Name", "Relation_to_UCSC_CpG_Island"), file.to.print.report = NULL)
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betas |
An (m by n) matrix of methylation values of $m$ methylation sites measured on $n$ individuals |
covariates |
A (n by p) vectors of adjusting covariates, ordered so that its rows corresponds to the columns of the ‘betas’ matrix. |
exposure |
A vector of size $n$ of exposure values for each individual. Same order as the covariates. |
id |
A vector of size $n$ of the IDs of the individual. The IDs should match the column names of the matrix ‘betas’. |
clusters.GEE.results |
A matrix of results from a GEE analysis of clusters. |
clusters.GEE.results.file |
A file with the results from a GEE analysis of clusters (if clusters.GEE.results is not given) |
minimum.sites |
A minimum number of sites in a cluster to be considered in the analysis. |
top.number |
The required number of top clusters to be reported. |
cutoff.fdr.pval |
A significance p-value threshold (after FDR correction). Only clusters with p-value smaller than cutoff.fdr.pval will be reported. |
cutoff.effect.size |
An effect size threshold. Only clusters with estimated effect size larger than cutoff.effect.size will be reported. |
annot |
annotation data table. The package uses the Illumina annotation file “illumina_450_menifest_v.1.2". |
annotation.file.name |
A name of annotation file to read. By default it is not required, since one can use ‘annot’, which is in the package. |
required.annotation |
What is the annotation to be reported on each of the sites in the reported clusters? |
file.to.print.report |
File name to print tables of annotation, effect sizes, and individual site analyses of sites in the top clusters. |
top.clusters |
A data frame summarizing the GEE results (exposure effect estimates, etc) of the top clusters |
annotation.top.clusters |
Annotations of the sites from the top clusters |
individual.sites.analysis |
Results of individual sites analysis, of the sites in the top clusters. |
Individual sites analysis uses the robust standard error.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | data(betas.7)
exposure <- rbinom(ncol(betas.7), 1,prob = 0.5) ## generate random exposure
covariates <- matrix(rnorm(2*ncol(betas.7)), ncol = 2)
rownames(covariates) <- colnames(betas.7)
## not run! to create new annotation file from the
## IlluminaHumanMethylation450k.db package:
## annot <- create.annot.triche(rownames(betas.7)
data(annot)
clusters.list <- assign.to.clusters(betas.7, annot)
GEE.results.clusters <- GEE.clusters(betas.7, clusters.list, exposure, covariates, id = colnames(betas.7), working.cor = "ex")
top.clusters.summary <- summarize.top.clusters(betas.7, covariates, exposure, id = colnames(betas.7), GEE.results.clusters, "results.tex", annot= annot)
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