asMethBlocks: Collapse a GenomicRatioSet or similar over methylation blocks...

In ttriche/sesamizeGEO: the poor man's methylation suite (cf. `sesamizer`)

Collapse a GenomicRatioSet or similar over methylation blocks (per Kaplan)

Description

By default, data(methBlocks) is used for summarization, singleton probes are included, methylation block rownames are returned against hg19, and neither singletons (!proper) nor unstable mappings (!stable) are filtered out.

Usage

asMethBlocks(x, g = c("hg19", "hg38"), proper = FALSE, stable = FALSE)

Arguments

x	a GenomicRatioSet or something like it
g	genome to use for methylation block coordinates (hg19)
proper	restrict to methylation blocks defined in Kaplan? (FALSE)
stable	restrict to sites/blocks shared across hg19 & hg38? (FALSE)

Details

stable is a weird flag and you probably should not use it. If and only if a probe maps to the same region in hg19 and hg38, it is deemed stable. That region can be one base pair wide, or it can be a thousand base pairs wide. The point is that this set of mappings is very small (about 4000 probes).

Value

     an object with same colData but with new rowRanges & assays

See Also

    switchMethBlocksGenome

ttriche/sesamizeGEO documentation built on Nov. 12, 2023, 5:42 p.m.