Description Usage Arguments Value Examples
Returns a list of matrices with annotations of the CpG sites represented by vector of probe names. Each vector represent a cluster
1 | annot.clusters(clusters.list, annot = NULL, annotation.file.name = NULL, required.annotation = c("IlmnID", "Coordinate_37", "UCSC_RefGene_Name", "UCSC_RefGene_Group", "UCSC_CpG_Islands_Name", "Relation_to_UCSC_CpG_Island"))
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clusters.list |
A list in which each element is a vector of illumine probe names. |
annot |
A preloaded data.table of annotation |
annotation.file.name |
If annot it not given, annotation.file.name can be provide the file name of the illumine annotation file and the function will load it and convert it to a data.table. If neither annot or annotation.file.name are provided, annotation will be loaded from a Tim Triche's bioconductor R package. |
required.annotation |
Names of columns from Illumina annotation file, to be provided as annotation |
A list corresponding to clusters.list. Each element in the list is matrix of required.annotations for each of the probes in the vector in the corresponding element in clusters.list.
1 2 3 4 5 6 7 8 | data(betas.7) ## upload methylation data
exposure <- rbinom(ncol(betas.7), 1,prob = 0.5) ## generate random exposure
covariates <- matrix(rnorm(2*ncol(betas.7)), ncol = 2)
data(annot.7)
clusters.list <- assign.to.clusters(betas.7, annot.7)
annotated.clusters <- annot.clusters(clusters.list[1:10], annot = annot.7, required.annotation = c("IlmnID", "Coordinate_37", "UCSC_RefGene_Name", "UCSC_RefGene_Group"))
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