Description Usage Arguments Details Value Examples
The matrix produces lists of ordered methylation matrices, according to location
1 | order.betas.by.chrom.location(betas, annot = NULL, annotation.file.name = NULL, return.chroms = NULL)
|
betas |
An (m by n) matrix of methylation values measured on $n$ participants in $m$ sites. |
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. |
return.chroms |
Optional list of chromosomes, if one is interested in specific chromosomes. |
Annotation: the package is adjusted to the Illumina annotation (i.e. through part of its column names) but could be easily adjusted to a an attestation data table with different column names.
sites.locations.by.chrom |
A list ordered by chromosome number. Each item in this list contains a matrix specifying chromosomal locations of each of the sites in the subsets of sites from betas from the corresponding chromosome. The rows are organized according to chromosomal location. |
1 2 3 4 5 6 |
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